PTox-WP2: MultiQC Report

General Statistics

Showing ¹²⁸/₁₂₈ rows and ²²/₄₅ columns.

Sample Name	5'-3' bias	M Aligned	Exonic	Intronic	Intergenic	Overlapping Exon	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Mean insert	Reads	Reads mapped	% Reads mapped	rRNA	Total reads	Aligned	Aligned	Uniq aligned	Uniq aligned	Multimapped	M Unique Reads	% Pass Dedup	Dups	GC	Avg len	Median len	Failed	Seqs	% > Q30	Mb Q30 bases	Reads After Filtering	GC content	% PF	% Adapter	Mean R1 Length	Dups	GC	Avg len	Median len	Failed	Seqs
CTL_0_S2_P1_R2_93_HG03111_ESN	0.97	0.7M	0.3M	0.2M	0.0M	0.1M	0.53%	0.4M	0.7M	100.0%	0.0%	5.8%	0.7M	0.0bp	1.1M	1.1M	100.0%	12.8%	4.4M	4.1M	93.6%	3.4M	78.5%	0.7M	1.1M	19.4%	64.4%	44.0%	151bp	151bp	27%	6.8M	89.3%	519.1Mb	5.0M	40.6%	73.2%	38.9%	141.0bp	79.6%	40.0%	116bp	141bp	18%	5.0M
CTL_0_S2_P1_R2_115_HG03162_ESN	0.76	1.7M	0.8M	0.5M	0.1M	0.2M	0.47%	0.8M	1.7M	100.0%	0.0%	3.9%	1.7M	0.0bp	2.5M	2.5M	100.0%	17.9%	6.1M	5.9M	95.7%	4.9M	80.8%	0.9M	2.5M	30.9%	55.7%	41.0%	151bp	151bp	27%	8.7M	89.4%	770.0Mb	7.4M	40.8%	85.7%	33.4%	141.0bp	70.9%	40.0%	116bp	141bp	27%	7.4M
CTL_0_S2_P1_R2_166_HG03517_ESN	1.03	0.5M	0.2M	0.1M	0.0M	0.1M	0.54%	0.3M	0.5M	100.0%	0.0%	5.1%	0.5M	0.0bp	0.7M	0.7M	100.0%	12.0%	4.0M	3.9M	95.8%	3.3M	81.2%	0.6M	0.7M	14.2%	74.7%	42.0%	151bp	151bp	27%	5.3M	90.6%	498.6Mb	4.6M	42.0%	85.6%	29.4%	141.0bp	84.7%	41.0%	120bp	141bp	18%	4.6M
CTL_0_S2_P1_R2_194_GM18505_YRI	0.82	1.1M	0.5M	0.3M	0.1M	0.1M	0.51%	0.6M	1.1M	100.0%	0.0%	4.9%	1.1M	0.0bp	1.7M	1.7M	100.0%	19.1%	6.7M	6.4M	95.8%	5.4M	81.3%	1.0M	1.7M	19.3%	69.8%	41.0%	151bp	151bp	27%	9.6M	89.5%	849.3Mb	8.3M	40.9%	86.2%	35.4%	141.0bp	81.3%	40.0%	115bp	141bp	27%	8.3M
CTL_0_S2_P1_R2_197_GM18511_YRI	1.64	0.3M	0.1M	0.1M	0.0M	0.0M	0.60%	0.2M	0.3M	100.0%	0.0%	8.3%	0.3M	0.0bp	0.5M	0.5M	100.0%	11.5%	3.0M	2.7M	90.7%	2.2M	74.8%	0.5M	0.5M	12.9%	69.3%	45.0%	151bp	151bp	27%	4.8M	89.9%	349.3Mb	3.4M	41.7%	69.9%	41.8%	141.0bp	85.6%	41.0%	115bp	141bp	18%	3.4M
CTL_0_S2_P1_R2_199_GM18517_YRI	0.83	0.5M	0.2M	0.1M	0.0M	0.0M	0.54%	0.3M	0.5M	100.0%	0.0%	6.0%	0.5M	0.0bp	0.8M	0.8M	100.0%	13.1%	3.5M	3.3M	92.8%	2.7M	77.5%	0.5M	0.8M	16.9%	65.9%	45.0%	151bp	151bp	27%	5.5M	89.8%	418.6Mb	4.0M	41.8%	73.2%	40.8%	141.0bp	81.8%	41.0%	115bp	141bp	18%	4.0M
CTL_0_S2_P1_R2_201_GM18520_YRI	0.90	0.2M	0.1M	0.1M	0.0M	0.0M	0.58%	0.3M	0.2M	100.0%	0.0%	9.9%	0.2M	0.0bp	0.5M	0.5M	100.0%	12.2%	2.9M	2.5M	86.3%	2.0M	70.0%	0.5M	0.5M	13.4%	66.0%	48.0%	151bp	151bp	27%	5.6M	88.7%	326.2Mb	3.3M	41.0%	59.5%	48.0%	141.0bp	83.5%	40.0%	111bp	141bp	18%	3.3M
CTL_0_S2_P1_R2_203_GM18523_YRI	0.88	0.8M	0.3M	0.2M	0.1M	0.1M	0.52%	0.5M	0.8M	100.0%	0.0%	5.5%	0.8M	0.0bp	1.3M	1.3M	100.0%	18.0%	3.8M	3.4M	91.1%	2.8M	75.8%	0.6M	1.3M	25.7%	55.4%	47.0%	151bp	151bp	27%	7.0M	89.1%	445.5Mb	4.6M	41.6%	65.8%	50.5%	141.0bp	75.1%	41.0%	109bp	141bp	27%	4.6M
CTL_0_S2_P1_R2_212_GM18873_YRI	0.92	0.6M	0.2M	0.2M	0.0M	0.1M	0.54%	0.4M	0.6M	100.0%	0.0%	6.9%	0.6M	0.0bp	1.0M	1.0M	100.0%	15.6%	4.8M	4.3M	90.8%	3.6M	75.5%	0.7M	1.0M	15.7%	65.6%	48.0%	151bp	151bp	27%	8.5M	89.6%	549.4Mb	5.7M	42.7%	66.6%	52.0%	141.0bp	82.7%	42.0%	108bp	141bp	27%	5.7M
CTL_0_S2_P1_R2_216_GM18878_YRI	7.30	0.1M	0.0M	0.0M	0.0M	0.0M	1.25%	0.3M	0.1M	100.0%	0.0%	22.0%	0.1M	0.0bp	0.4M	0.4M	100.0%	4.9%	1.1M	0.5M	45.2%	0.2M	18.1%	0.3M	0.4M	30.3%	46.0%	57.0%	151bp	151bp	27%	5.3M	77.0%	48.5Mb	1.1M	41.3%	20.8%	83.9%	141.0bp	59.4%	41.0%	57bp	37bp	45%	1.1M
CTL_0_S2_P1_R2_220_GM18909_YRI	1.07	0.4M	0.2M	0.1M	0.0M	0.0M	0.54%	0.2M	0.4M	100.0%	0.0%	5.8%	0.4M	0.0bp	0.6M	0.6M	100.0%	10.2%	3.2M	3.0M	94.0%	2.6M	80.2%	0.4M	0.6M	14.6%	71.3%	43.0%	151bp	151bp	27%	4.5M	90.5%	388.4Mb	3.6M	41.8%	79.5%	34.7%	141.0bp	84.2%	41.0%	119bp	141bp	18%	3.6M
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	0.70	1.4M	0.6M	0.5M	0.1M	0.1M	0.48%	0.6M	1.4M	100.0%	0.0%	3.8%	1.4M	0.0bp	2.1M	2.1M	100.0%	13.6%	7.2M	7.0M	97.0%	6.0M	83.2%	1.0M	2.1M	22.1%	67.6%	40.0%	151bp	151bp	27%	9.2M	89.8%	877.6Mb	8.3M	40.3%	90.5%	30.1%	141.0bp	77.9%	40.0%	117bp	141bp	18%	8.3M
CTL_0_S2_P1_R2_228_GM18933_YRI	0.93	0.7M	0.3M	0.2M	0.0M	0.1M	0.54%	0.4M	0.7M	100.0%	0.0%	5.1%	0.7M	0.0bp	1.1M	1.1M	100.0%	14.7%	5.0M	4.7M	95.1%	4.0M	80.3%	0.7M	1.1M	16.8%	69.5%	43.0%	151bp	151bp	36%	7.3M	89.8%	607.5Mb	5.8M	41.5%	80.6%	36.8%	141.0bp	82.4%	41.0%	116bp	141bp	27%	5.8M
CTL_0_S2_P1_R2_236_GM19095_YRI	1.25	0.3M	0.1M	0.1M	0.0M	0.0M	0.61%	0.3M	0.3M	100.0%	0.0%	7.6%	0.3M	0.0bp	0.6M	0.6M	100.0%	11.2%	3.0M	2.7M	89.7%	2.2M	74.9%	0.4M	0.6M	15.6%	64.8%	47.0%	151bp	151bp	27%	5.2M	89.3%	337.7Mb	3.4M	41.5%	65.0%	47.4%	141.0bp	82.3%	41.0%	112bp	141bp	18%	3.4M
CTL_0_S2_P1_R2_239_GM19099_YRI	1.28	0.4M	0.1M	0.1M	0.0M	0.0M	0.62%	0.4M	0.4M	100.0%	0.0%	9.7%	0.4M	0.0bp	0.7M	0.7M	100.0%	8.8%	3.3M	2.8M	83.6%	2.2M	67.0%	0.6M	0.7M	16.9%	59.2%	51.0%	151bp	151bp	27%	7.7M	88.7%	335.3Mb	3.6M	41.8%	47.3%	61.0%	141.0bp	79.7%	41.0%	104bp	137bp	18%	3.6M
CTL_0_S2_P1_R2_240_GM19102_YRI	0.94	0.7M	0.3M	0.2M	0.0M	0.1M	0.52%	0.5M	0.7M	100.0%	0.0%	6.3%	0.7M	0.0bp	1.2M	1.2M	100.0%	11.6%	5.0M	4.6M	90.8%	3.8M	74.9%	0.8M	1.2M	18.4%	61.7%	46.0%	151bp	151bp	27%	8.9M	89.5%	575.3Mb	5.7M	41.2%	63.8%	47.4%	141.0bp	79.6%	41.0%	113bp	141bp	18%	5.7M
CTL_0_S2_P1_R3_93_HG03111_ESN	1.33	0.2M	0.1M	0.1M	0.0M	0.0M	0.58%	0.1M	0.2M	100.0%	0.0%	5.7%	0.2M	0.0bp	0.3M	0.3M	100.0%	11.1%	3.4M	3.2M	94.4%	2.8M	82.2%	0.4M	0.3M	8.0%	80.7%	43.0%	151bp	151bp	27%	4.6M	91.3%	413.7Mb	3.8M	41.7%	83.1%	32.4%	141.0bp	90.0%	41.0%	120bp	141bp	18%	3.8M
CTL_0_S2_P1_R3_115_HG03162_ESN	0.74	1.2M	0.6M	0.3M	0.1M	0.1M	0.48%	0.6M	1.2M	100.0%	0.0%	4.1%	1.2M	0.0bp	1.8M	1.8M	100.0%	20.2%	6.5M	6.3M	97.0%	5.4M	82.5%	0.9M	1.8M	21.1%	68.0%	42.0%	151bp	151bp	27%	9.1M	90.4%	851.7Mb	8.2M	42.1%	89.6%	32.7%	141.0bp	80.5%	42.0%	116bp	141bp	27%	8.2M
CTL_0_S2_P1_R3_166_HG03517_ESN	0.77	0.4M	0.2M	0.1M	0.0M	0.0M	0.52%	0.3M	0.4M	100.0%	0.0%	5.6%	0.4M	0.0bp	0.7M	0.7M	100.0%	16.2%	4.5M	4.4M	96.1%	3.8M	82.6%	0.6M	0.7M	12.5%	78.8%	41.0%	151bp	151bp	27%	6.1M	90.9%	588.5Mb	5.4M	41.8%	89.3%	28.2%	141.0bp	87.1%	41.0%	120bp	141bp	27%	5.4M
CTL_0_S2_P1_R3_194_GM18505_YRI	0.82	0.6M	0.3M	0.2M	0.0M	0.1M	0.51%	0.4M	0.6M	100.0%	0.0%	5.7%	0.6M	0.0bp	1.0M	1.0M	100.0%	13.9%	6.3M	6.0M	95.7%	5.2M	82.6%	0.8M	1.0M	11.9%	78.0%	42.0%	151bp	151bp	27%	8.4M	91.6%	795.0Mb	7.3M	41.9%	86.9%	31.2%	141.0bp	87.4%	41.0%	118bp	141bp	27%	7.3M
CTL_0_S2_P1_R3_197_GM18511_YRI	1.48	0.3M	0.1M	0.1M	0.0M	0.0M	0.56%	0.3M	0.3M	100.0%	0.0%	7.3%	0.3M	0.0bp	0.6M	0.6M	100.0%	12.4%	4.0M	3.7M	92.8%	3.1M	78.2%	0.6M	0.6M	12.2%	73.6%	44.0%	151bp	151bp	27%	5.8M	91.0%	492.7Mb	4.6M	42.2%	78.8%	36.1%	141.0bp	86.5%	42.0%	118bp	141bp	18%	4.6M
CTL_0_S2_P1_R3_199_GM18517_YRI	1.13	0.2M	0.1M	0.0M	0.0M	0.0M	0.57%	0.2M	0.2M	100.0%	0.0%	6.7%	0.2M	0.0bp	0.4M	0.4M	100.0%	12.1%	3.2M	3.0M	93.5%	2.5M	78.0%	0.5M	0.4M	8.6%	76.9%	45.0%	151bp	151bp	27%	4.9M	90.9%	391.1Mb	3.7M	42.4%	74.5%	37.0%	141.0bp	89.6%	42.0%	117bp	141bp	18%	3.7M
CTL_0_S2_P1_R3_201_GM18520_YRI	0.84	1.6M	0.8M	0.4M	0.1M	0.2M	0.44%	0.8M	1.6M	100.0%	0.0%	4.0%	1.6M	0.0bp	2.3M	2.3M	100.0%	16.0%	8.2M	8.0M	97.3%	6.6M	80.3%	1.4M	2.3M	21.0%	67.4%	40.0%	151bp	151bp	27%	10.8M	90.3%	1034.4Mb	9.8M	40.8%	89.9%	30.2%	141.0bp	79.1%	40.0%	118bp	141bp	18%	9.8M
CTL_0_S2_P1_R3_203_GM18523_YRI	1.85	0.4M	0.1M	0.1M	0.0M	0.0M	0.57%	0.4M	0.4M	100.0%	0.0%	8.8%	0.4M	0.0bp	0.7M	0.7M	100.0%	18.1%	3.1M	2.5M	80.7%	2.0M	64.5%	0.5M	0.7M	19.0%	57.9%	53.0%	151bp	151bp	27%	9.5M	88.5%	326.1Mb	3.7M	41.9%	39.5%	69.0%	141.0bp	79.2%	41.0%	98bp	112bp	18%	3.7M
CTL_0_S2_P1_R3_212_GM18873_YRI	0.94	0.5M	0.2M	0.1M	0.0M	0.1M	0.51%	0.3M	0.5M	100.0%	0.0%	5.6%	0.5M	0.0bp	0.8M	0.8M	100.0%	13.8%	5.2M	4.9M	94.6%	4.2M	80.4%	0.7M	0.8M	12.4%	73.7%	45.0%	151bp	151bp	27%	7.7M	91.4%	641.0Mb	6.1M	42.9%	78.7%	40.0%	141.0bp	86.4%	42.0%	116bp	141bp	27%	6.1M
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	1.01	0.4M	0.2M	0.1M	0.0M	0.0M	0.55%	0.4M	0.4M	100.0%	0.0%	8.5%	0.4M	0.0bp	0.8M	0.8M	100.0%	13.7%	5.3M	4.8M	89.5%	3.9M	73.3%	0.9M	0.8M	12.0%	68.3%	49.0%	151bp	151bp	27%	9.5M	91.1%	620.7Mb	6.2M	43.5%	65.2%	50.4%	141.0bp	85.6%	43.0%	110bp	141bp	27%	6.2M
CTL_0_S2_P1_R3_220_GM18909_YRI	1.15	0.3M	0.1M	0.1M	0.0M	0.0M	0.59%	0.4M	0.3M	100.0%	0.0%	9.9%	0.3M	0.0bp	0.7M	0.7M	100.0%	10.1%	5.1M	4.5M	87.4%	3.7M	71.5%	0.8M	0.7M	10.6%	69.3%	49.0%	151bp	151bp	27%	9.0M	90.6%	576.9Mb	5.7M	42.9%	63.7%	48.8%	141.0bp	86.1%	42.0%	111bp	141bp	18%	5.7M
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	nan	0.2M	0.0M	0.0M	0.0M	0.0M	1.58%	0.4M	0.2M	100.0%	0.0%	23.2%	0.2M	0.0bp	0.6M	0.6M	100.0%	4.2%	1.4M	0.5M	35.1%	0.2M	11.6%	0.3M	0.6M	34.3%	45.0%	58.0%	151bp	151bp	27%	6.9M	72.9%	62.2Mb	1.5M	41.2%	21.5%	80.0%	141.0bp	55.7%	41.0%	57bp	42bp	45%	1.5M
CTL_0_S2_P1_R3_228_GM18933_YRI	1.03	0.3M	0.1M	0.1M	0.0M	0.0M	0.60%	0.3M	0.3M	100.0%	0.0%	8.9%	0.3M	0.0bp	0.7M	0.7M	100.0%	9.7%	4.8M	4.3M	89.5%	3.6M	74.4%	0.7M	0.7M	10.5%	70.2%	47.0%	151bp	151bp	27%	7.9M	90.7%	559.5Mb	5.4M	42.6%	67.7%	44.4%	141.0bp	86.4%	42.0%	115bp	141bp	18%	5.4M
CTL_0_S2_P1_R3_236_GM19095_YRI	0.83	0.7M	0.3M	0.2M	0.1M	0.1M	0.52%	0.4M	0.7M	100.0%	0.0%	5.0%	0.7M	0.0bp	1.1M	1.1M	100.0%	13.1%	6.3M	6.0M	95.5%	5.1M	82.0%	0.8M	1.1M	14.3%	74.4%	43.0%	151bp	151bp	27%	8.4M	91.1%	776.3Mb	7.2M	42.1%	85.3%	32.5%	141.0bp	84.8%	42.0%	118bp	141bp	27%	7.2M
CTL_0_S2_P1_R3_239_GM19099_YRI	nan	0.2M	0.0M	0.0M	0.0M	0.0M	1.55%	0.4M	0.2M	100.0%	0.0%	22.3%	0.2M	0.0bp	0.6M	0.6M	100.0%	7.3%	1.4M	0.6M	40.5%	0.2M	13.0%	0.4M	0.6M	29.3%	50.7%	62.0%	151bp	151bp	45%	7.6M	72.3%	60.0Mb	1.5M	43.3%	20.4%	81.7%	141.0bp	60.9%	43.0%	54bp	37bp	45%	1.5M
CTL_0_S2_P1_R3_240_GM19102_YRI	0.92	0.8M	0.3M	0.3M	0.1M	0.1M	0.49%	0.5M	0.8M	100.0%	0.0%	5.5%	0.8M	0.0bp	1.4M	1.4M	100.0%	9.3%	5.4M	5.1M	93.0%	4.3M	78.8%	0.8M	1.4M	19.1%	64.4%	48.0%	151bp	151bp	36%	8.2M	91.2%	626.8Mb	6.0M	42.6%	73.6%	44.3%	141.0bp	78.9%	42.0%	115bp	141bp	18%	6.0M
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	1.07	0.3M	0.1M	0.1M	0.0M	0.0M	0.59%	0.4M	0.3M	100.0%	0.0%	10.2%	0.3M	0.0bp	0.7M	0.7M	100.0%	11.4%	3.6M	3.0M	84.1%	2.4M	67.5%	0.6M	0.7M	15.6%	61.5%	48.0%	151bp	151bp	36%	7.0M	88.1%	386.6Mb	4.0M	41.0%	57.6%	51.5%	141.0bp	80.9%	41.0%	109bp	141bp	18%	4.0M
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	0.73	1.7M	0.7M	0.6M	0.1M	0.2M	0.47%	0.7M	1.7M	100.0%	0.0%	3.5%	1.7M	0.0bp	2.4M	2.4M	100.0%	17.4%	7.1M	6.9M	96.7%	5.9M	83.3%	0.9M	2.4M	26.1%	64.1%	40.0%	151bp	151bp	27%	9.4M	89.8%	899.5Mb	8.6M	40.5%	91.8%	31.0%	141.0bp	74.9%	40.0%	116bp	141bp	27%	8.6M
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	0.87	0.5M	0.2M	0.1M	0.0M	0.0M	0.53%	0.4M	0.5M	100.0%	0.0%	6.1%	0.5M	0.0bp	0.9M	0.9M	100.0%	14.9%	4.4M	4.2M	93.7%	3.5M	79.1%	0.6M	0.9M	15.4%	71.0%	44.0%	151bp	151bp	27%	6.5M	89.5%	541.8Mb	5.2M	41.4%	80.3%	35.6%	141.0bp	83.4%	41.0%	116bp	141bp	18%	5.2M
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	1.12	0.5M	0.2M	0.1M	0.0M	0.0M	0.54%	0.4M	0.5M	100.0%	0.0%	6.1%	0.5M	0.0bp	0.9M	0.9M	100.0%	14.4%	3.6M	3.4M	92.9%	2.9M	79.0%	0.5M	0.9M	18.4%	66.3%	45.0%	151bp	151bp	27%	5.6M	89.7%	432.4Mb	4.2M	41.2%	75.9%	40.2%	141.0bp	81.0%	41.0%	114bp	141bp	18%	4.2M
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	0.98	0.5M	0.2M	0.1M	0.0M	0.0M	0.54%	0.4M	0.5M	100.0%	0.0%	7.0%	0.5M	0.0bp	0.8M	0.8M	100.0%	13.0%	5.4M	5.0M	92.3%	4.2M	78.6%	0.7M	0.8M	12.0%	73.0%	44.0%	151bp	151bp	27%	8.1M	89.9%	644.2Mb	6.2M	41.1%	76.7%	37.6%	141.0bp	86.1%	41.0%	116bp	141bp	18%	6.2M
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	0.90	0.3M	0.1M	0.1M	0.0M	0.0M	0.59%	0.3M	0.3M	100.0%	0.0%	8.9%	0.3M	0.0bp	0.7M	0.7M	100.0%	13.0%	3.2M	2.8M	86.6%	2.3M	70.2%	0.5M	0.7M	16.2%	62.3%	48.0%	151bp	151bp	27%	6.5M	88.7%	357.0Mb	3.7M	41.0%	57.5%	53.4%	141.0bp	81.4%	40.0%	108bp	141bp	18%	3.7M
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	0.85	0.4M	0.2M	0.1M	0.0M	0.0M	0.52%	0.3M	0.4M	100.0%	0.0%	6.4%	0.4M	0.0bp	0.7M	0.7M	100.0%	12.4%	3.2M	3.0M	91.7%	2.5M	77.1%	0.5M	0.7M	17.0%	66.1%	45.0%	151bp	151bp	27%	5.2M	89.6%	373.6Mb	3.7M	41.1%	70.6%	44.5%	141.0bp	81.5%	41.0%	113bp	141bp	18%	3.7M
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	0.73	1.6M	0.7M	0.5M	0.1M	0.1M	0.49%	0.7M	1.6M	100.0%	0.0%	3.5%	1.6M	0.0bp	2.4M	2.4M	100.0%	18.9%	6.8M	6.5M	95.9%	5.5M	80.6%	1.0M	2.4M	26.7%	59.0%	42.0%	151bp	151bp	27%	10.0M	89.1%	850.6Mb	8.4M	40.4%	84.1%	37.7%	141.0bp	74.5%	40.0%	113bp	141bp	27%	8.4M
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	0.73	0.7M	0.3M	0.1M	0.0M	0.1M	0.48%	0.4M	0.7M	100.0%	0.0%	5.4%	0.7M	0.0bp	1.1M	1.1M	100.0%	19.2%	5.1M	4.8M	93.5%	4.1M	79.3%	0.7M	1.1M	16.3%	69.4%	42.0%	151bp	151bp	27%	8.1M	89.3%	651.5Mb	6.3M	40.9%	78.1%	37.8%	141.0bp	83.0%	40.0%	115bp	141bp	27%	6.3M
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	2.51	0.2M	0.0M	0.0M	0.0M	0.0M	0.85%	0.3M	0.2M	100.0%	0.0%	17.5%	0.2M	0.0bp	0.5M	0.5M	100.0%	14.5%	2.7M	1.6M	60.4%	1.1M	41.9%	0.5M	0.5M	15.8%	56.1%	54.0%	151bp	151bp	36%	10.6M	83.0%	229.5Mb	3.1M	39.7%	29.5%	69.7%	141.0bp	77.7%	39.0%	89bp	87bp	27%	3.1M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	0.79	0.4M	0.2M	0.1M	0.0M	0.0M	0.51%	0.2M	0.4M	100.0%	0.0%	4.9%	0.4M	0.0bp	0.6M	0.6M	100.0%	12.1%	4.9M	4.6M	95.0%	4.0M	82.4%	0.6M	0.6M	10.3%	77.5%	43.0%	151bp	151bp	27%	6.7M	90.5%	598.0Mb	5.5M	41.3%	82.5%	32.6%	141.0bp	87.9%	41.0%	120bp	141bp	18%	5.5M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	0.83	0.6M	0.3M	0.2M	0.0M	0.1M	0.52%	0.4M	0.6M	100.0%	0.0%	5.4%	0.6M	0.0bp	1.0M	1.0M	100.0%	12.8%	6.4M	6.0M	94.7%	5.2M	82.0%	0.8M	1.0M	12.7%	74.5%	43.0%	151bp	151bp	27%	8.9M	90.2%	774.8Mb	7.3M	41.2%	81.9%	34.4%	141.0bp	85.9%	41.0%	118bp	141bp	18%	7.3M
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	0.88	0.7M	0.3M	0.2M	0.0M	0.1M	0.51%	0.4M	0.7M	100.0%	0.0%	4.8%	0.7M	0.0bp	1.0M	1.0M	100.0%	13.5%	5.4M	5.2M	95.2%	4.4M	82.0%	0.7M	1.0M	14.8%	72.0%	42.0%	151bp	151bp	27%	7.7M	90.2%	664.2Mb	6.3M	40.6%	81.1%	34.7%	141.0bp	84.1%	40.0%	117bp	141bp	18%	6.3M
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	0.79	0.5M	0.2M	0.2M	0.0M	0.0M	0.53%	0.3M	0.5M	100.0%	0.0%	5.0%	0.5M	0.0bp	0.8M	0.8M	100.0%	13.5%	4.2M	3.9M	93.9%	3.4M	81.0%	0.5M	0.8M	16.0%	69.2%	45.0%	151bp	151bp	36%	6.2M	89.7%	506.8Mb	4.8M	41.4%	78.3%	36.5%	141.0bp	82.2%	41.0%	117bp	141bp	18%	4.8M
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	0.89	0.6M	0.3M	0.2M	0.0M	0.1M	0.50%	0.3M	0.6M	100.0%	0.0%	4.8%	0.6M	0.0bp	1.0M	1.0M	100.0%	14.2%	4.5M	4.3M	94.4%	3.7M	81.2%	0.6M	1.0M	16.6%	67.6%	44.0%	151bp	151bp	27%	7.0M	89.9%	550.5Mb	5.3M	41.3%	75.7%	38.6%	141.0bp	82.2%	41.0%	116bp	141bp	18%	5.3M
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	0.96	0.5M	0.2M	0.1M	0.0M	0.0M	0.53%	0.4M	0.5M	100.0%	0.0%	7.0%	0.5M	0.0bp	0.9M	0.9M	100.0%	12.5%	3.5M	3.1M	88.7%	2.6M	73.1%	0.5M	0.9M	18.9%	59.0%	48.0%	151bp	151bp	27%	7.0M	89.0%	399.7Mb	4.0M	41.0%	57.5%	50.4%	141.0bp	78.9%	41.0%	112bp	141bp	18%	4.0M
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	0.88	0.4M	0.2M	0.1M	0.0M	0.0M	0.49%	0.2M	0.4M	100.0%	0.0%	5.1%	0.4M	0.0bp	0.6M	0.6M	100.0%	18.0%	4.6M	4.4M	96.5%	3.8M	82.6%	0.6M	0.6M	10.4%	79.6%	41.0%	151bp	151bp	27%	6.5M	90.9%	605.8Mb	5.6M	41.6%	86.2%	28.5%	141.0bp	88.9%	41.0%	119bp	141bp	27%	5.6M
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	0.98	0.4M	0.2M	0.1M	0.0M	0.0M	0.51%	0.3M	0.4M	100.0%	0.0%	6.4%	0.4M	0.0bp	0.7M	0.7M	100.0%	16.3%	4.0M	3.8M	94.0%	3.2M	79.0%	0.6M	0.7M	13.2%	72.6%	44.0%	151bp	151bp	27%	6.1M	90.6%	513.1Mb	4.8M	43.0%	79.1%	34.1%	141.0bp	86.1%	42.0%	118bp	141bp	27%	4.8M
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	1.01	0.4M	0.2M	0.1M	0.0M	0.0M	0.52%	0.2M	0.4M	100.0%	0.0%	5.5%	0.4M	0.0bp	0.6M	0.6M	100.0%	16.2%	4.7M	4.5M	95.8%	3.9M	82.2%	0.6M	0.6M	9.5%	79.8%	43.0%	151bp	151bp	27%	6.7M	91.4%	611.3Mb	5.6M	42.4%	84.2%	32.0%	141.0bp	89.4%	42.0%	119bp	141bp	27%	5.6M
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	0.97	0.4M	0.2M	0.1M	0.0M	0.0M	0.51%	0.3M	0.4M	100.0%	0.0%	6.6%	0.4M	0.0bp	0.8M	0.8M	100.0%	15.9%	5.5M	5.1M	93.9%	4.4M	79.7%	0.8M	0.8M	10.7%	77.4%	44.0%	151bp	151bp	27%	7.9M	90.6%	686.2Mb	6.5M	41.7%	81.9%	33.8%	141.0bp	88.0%	41.0%	117bp	141bp	27%	6.5M
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	1.04	0.2M	0.1M	0.1M	0.0M	0.0M	0.59%	0.2M	0.2M	100.0%	0.0%	9.1%	0.2M	0.0bp	0.5M	0.5M	100.0%	12.7%	3.2M	2.9M	89.9%	2.4M	75.3%	0.5M	0.5M	11.2%	71.7%	47.0%	151bp	151bp	27%	5.3M	90.8%	379.7Mb	3.7M	42.4%	70.1%	44.4%	141.0bp	87.2%	42.0%	113bp	141bp	18%	3.7M
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	0.99	0.4M	0.2M	0.1M	0.0M	0.0M	0.56%	0.4M	0.4M	100.0%	0.0%	7.9%	0.4M	0.0bp	0.8M	0.8M	100.0%	15.2%	5.4M	5.0M	92.0%	4.2M	76.7%	0.8M	0.8M	11.3%	74.0%	45.0%	151bp	151bp	27%	8.4M	90.6%	660.9Mb	6.4M	42.4%	76.5%	40.8%	141.0bp	87.3%	42.0%	114bp	141bp	18%	6.4M
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	0.81	0.9M	0.4M	0.3M	0.1M	0.1M	0.47%	0.5M	0.9M	100.0%	0.0%	4.4%	0.9M	0.0bp	1.4M	1.4M	100.0%	18.3%	6.0M	5.8M	96.5%	4.9M	82.3%	0.9M	1.4M	17.8%	71.1%	42.0%	151bp	151bp	27%	8.4M	90.2%	770.2Mb	7.3M	41.7%	87.2%	33.5%	141.0bp	82.7%	41.0%	116bp	141bp	27%	7.3M
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	0.97	0.5M	0.2M	0.1M	0.0M	0.0M	0.52%	0.4M	0.5M	100.0%	0.0%	6.2%	0.5M	0.0bp	0.8M	0.8M	100.0%	17.8%	4.2M	3.8M	91.2%	3.2M	77.2%	0.6M	0.8M	15.9%	66.5%	47.0%	151bp	151bp	27%	7.0M	89.7%	514.3Mb	5.1M	42.6%	72.2%	42.7%	141.0bp	82.9%	42.0%	113bp	141bp	27%	5.1M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	0.84	0.6M	0.3M	0.1M	0.0M	0.1M	0.45%	0.4M	0.6M	100.0%	0.0%	5.1%	0.6M	0.0bp	1.0M	1.0M	100.0%	17.8%	7.2M	6.9M	96.3%	5.9M	82.2%	1.0M	1.0M	10.4%	79.3%	43.0%	151bp	151bp	27%	10.1M	91.0%	956.5Mb	8.7M	42.4%	86.3%	29.0%	141.0bp	89.0%	42.0%	120bp	141bp	27%	8.7M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	0.77	1.1M	0.5M	0.4M	0.1M	0.1M	0.46%	0.4M	1.1M	100.0%	0.0%	3.1%	1.1M	0.0bp	1.5M	1.5M	100.0%	11.3%	7.7M	7.5M	97.6%	6.7M	86.5%	0.9M	1.5M	15.5%	78.0%	40.0%	151bp	151bp	27%	9.1M	91.6%	970.2Mb	8.7M	41.3%	95.2%	24.7%	141.0bp	83.6%	41.0%	122bp	141bp	18%	8.7M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	0.70	0.7M	0.4M	0.2M	0.0M	0.1M	0.47%	0.3M	0.7M	100.0%	0.0%	3.9%	0.7M	0.0bp	1.1M	1.1M	100.0%	12.0%	6.8M	6.6M	97.4%	5.8M	84.7%	0.9M	1.1M	12.4%	80.7%	40.0%	151bp	151bp	27%	8.3M	91.5%	879.9Mb	7.7M	41.8%	93.4%	20.5%	141.0bp	86.7%	41.0%	124bp	141bp	18%	7.7M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	0.88	0.4M	0.2M	0.1M	0.0M	0.0M	0.52%	0.3M	0.4M	100.0%	0.0%	5.8%	0.4M	0.0bp	0.7M	0.7M	100.0%	9.8%	6.1M	5.7M	94.4%	5.0M	81.8%	0.8M	0.7M	9.7%	77.9%	44.0%	151bp	151bp	27%	8.2M	91.6%	744.7Mb	6.7M	41.9%	82.1%	32.3%	141.0bp	88.3%	41.0%	121bp	141bp	18%	6.7M
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	0.75	1.0M	0.4M	0.3M	0.1M	0.1M	0.48%	0.5M	1.0M	100.0%	0.0%	4.3%	1.0M	0.0bp	1.5M	1.5M	100.0%	12.6%	8.6M	8.3M	96.8%	7.2M	83.8%	1.1M	1.5M	13.6%	77.2%	41.0%	151bp	151bp	27%	11.0M	91.7%	1095.1Mb	9.8M	41.7%	89.6%	26.8%	141.0bp	85.7%	41.0%	122bp	141bp	18%	9.8M
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	0.75	0.2M	0.1M	0.0M	0.0M	0.0M	0.56%	0.2M	0.2M	100.0%	0.0%	8.0%	0.2M	0.0bp	0.4M	0.4M	100.0%	13.2%	3.4M	3.1M	91.8%	2.6M	77.3%	0.5M	0.4M	9.2%	73.0%	47.0%	151bp	151bp	27%	5.7M	91.1%	413.4Mb	3.9M	42.8%	68.0%	42.3%	141.0bp	89.1%	42.0%	116bp	141bp	27%	3.9M
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	0.77	0.4M	0.2M	0.1M	0.0M	0.0M	0.50%	0.3M	0.4M	100.0%	0.0%	6.7%	0.4M	0.0bp	0.7M	0.7M	100.0%	15.3%	4.5M	4.2M	93.2%	3.6M	78.8%	0.7M	0.7M	11.5%	73.0%	45.0%	151bp	151bp	27%	7.1M	91.0%	568.2Mb	5.3M	42.6%	74.8%	37.7%	141.0bp	87.1%	42.0%	117bp	141bp	27%	5.3M
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	0.97	0.4M	0.2M	0.1M	0.0M	0.0M	0.50%	0.4M	0.4M	100.0%	0.0%	8.6%	0.4M	0.0bp	0.8M	0.8M	100.0%	13.0%	4.0M	3.5M	86.1%	2.8M	69.5%	0.7M	0.8M	15.4%	60.2%	50.0%	151bp	151bp	36%	8.8M	89.5%	464.9Mb	4.6M	42.3%	52.5%	51.6%	141.0bp	81.8%	42.0%	112bp	141bp	18%	4.6M
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	0.85	0.2M	0.1M	0.0M	0.0M	0.0M	0.71%	0.3M	0.2M	100.0%	0.0%	13.2%	0.2M	0.0bp	0.6M	0.6M	100.0%	11.8%	2.6M	1.9M	73.0%	1.4M	54.1%	0.5M	0.6M	16.8%	56.5%	55.0%	151bp	151bp	27%	7.9M	85.4%	226.1Mb	2.9M	42.9%	37.2%	72.1%	141.0bp	76.2%	42.0%	90bp	87bp	27%	2.9M
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	1.18	0.6M	0.2M	0.1M	0.1M	0.0M	0.61%	0.6M	0.6M	100.0%	0.0%	8.6%	0.6M	0.0bp	1.1M	1.1M	100.0%	14.2%	4.7M	4.1M	86.6%	3.3M	69.4%	0.8M	1.1M	17.1%	62.1%	51.0%	151bp	151bp	27%	9.6M	88.6%	493.4Mb	5.5M	43.2%	57.4%	61.2%	141.0bp	80.1%	43.0%	101bp	122bp	18%	5.5M
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	2.14	0.2M	0.0M	0.0M	0.0M	0.0M	0.81%	0.4M	0.2M	100.0%	0.0%	15.5%	0.2M	0.0bp	0.6M	0.6M	100.0%	12.6%	2.7M	2.0M	74.1%	1.5M	55.0%	0.5M	0.6M	17.4%	57.9%	53.0%	151bp	151bp	27%	7.0M	85.6%	236.3Mb	3.0M	41.7%	43.3%	68.3%	141.0bp	79.0%	41.0%	91bp	92bp	27%	3.0M
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	1.01	0.3M	0.1M	0.1M	0.0M	0.0M	0.72%	0.4M	0.3M	100.0%	0.0%	12.3%	0.3M	0.0bp	0.6M	0.6M	100.0%	11.9%	3.2M	2.6M	81.0%	2.1M	64.4%	0.5M	0.6M	14.8%	61.1%	50.0%	151bp	151bp	36%	7.2M	87.9%	319.6Mb	3.6M	41.4%	50.5%	62.2%	141.0bp	81.5%	41.0%	100bp	122bp	18%	3.6M
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	1.19	0.3M	0.1M	0.1M	0.0M	0.0M	0.66%	0.4M	0.3M	100.0%	0.0%	11.3%	0.3M	0.0bp	0.7M	0.7M	100.0%	16.3%	3.6M	3.0M	81.7%	2.4M	66.3%	0.6M	0.7M	14.7%	62.5%	51.0%	151bp	151bp	27%	7.7M	87.7%	385.5Mb	4.3M	41.8%	56.3%	57.9%	141.0bp	81.8%	41.0%	101bp	122bp	18%	4.3M
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	0.81	0.6M	0.2M	0.2M	0.1M	0.0M	0.58%	0.4M	0.6M	100.0%	0.0%	6.3%	0.6M	0.0bp	1.0M	1.0M	100.0%	16.2%	3.9M	3.5M	90.4%	2.9M	75.5%	0.6M	1.0M	20.4%	60.9%	46.0%	151bp	151bp	27%	6.6M	89.0%	451.7Mb	4.6M	41.3%	69.9%	47.8%	141.0bp	78.5%	41.0%	110bp	141bp	18%	4.6M
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	0.61	0.2M	0.1M	0.0M	0.0M	0.0M	0.67%	0.3M	0.2M	100.0%	0.0%	12.7%	0.2M	0.0bp	0.5M	0.5M	100.0%	16.9%	2.5M	1.9M	78.3%	1.5M	60.5%	0.4M	0.5M	17.0%	58.9%	52.0%	151bp	151bp	36%	6.6M	85.9%	249.5Mb	3.0M	40.7%	45.2%	64.2%	141.0bp	79.6%	40.0%	98bp	117bp	18%	3.0M
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	0.31	0.2M	0.0M	0.0M	0.0M	0.0M	0.91%	0.4M	0.2M	100.0%	0.0%	17.9%	0.2M	0.0bp	0.6M	0.6M	100.0%	8.2%	2.2M	1.3M	60.1%	0.9M	40.3%	0.4M	0.6M	23.8%	52.3%	54.0%	151bp	151bp	36%	8.9M	82.8%	156.1Mb	2.4M	39.9%	27.0%	76.4%	141.0bp	70.7%	39.0%	79bp	77bp	36%	2.4M
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	0.81	0.2M	0.1M	0.0M	0.0M	0.0M	0.72%	0.3M	0.2M	100.0%	0.0%	12.9%	0.2M	0.0bp	0.5M	0.5M	100.0%	13.8%	2.6M	1.9M	74.5%	1.5M	59.1%	0.4M	0.5M	14.6%	60.0%	56.0%	151bp	151bp	27%	8.0M	86.0%	254.2Mb	3.0M	42.7%	37.7%	68.5%	141.0bp	80.8%	42.0%	97bp	112bp	27%	3.0M
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	0.36	0.1M	0.0M	0.0M	0.0M	0.0M	0.94%	0.3M	0.1M	100.0%	0.0%	19.7%	0.1M	0.0bp	0.4M	0.4M	100.0%	3.3%	1.6M	0.8M	52.7%	0.5M	33.7%	0.3M	0.4M	21.6%	52.5%	57.0%	151bp	151bp	36%	7.7M	81.6%	98.2Mb	1.6M	41.9%	21.2%	78.4%	141.0bp	68.6%	41.0%	74bp	72bp	36%	1.6M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	0.99	0.2M	0.1M	0.0M	0.0M	0.0M	0.71%	0.3M	0.2M	100.0%	0.0%	12.6%	0.2M	0.0bp	0.5M	0.5M	100.0%	14.8%	3.8M	3.1M	81.0%	2.5M	64.3%	0.6M	0.5M	11.0%	64.5%	50.0%	151bp	151bp	36%	9.7M	87.1%	395.1Mb	4.5M	40.9%	46.3%	63.1%	141.0bp	85.4%	40.0%	101bp	122bp	18%	4.5M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	0.84	0.2M	0.1M	0.0M	0.0M	0.0M	0.69%	0.3M	0.2M	100.0%	0.0%	12.6%	0.2M	0.0bp	0.6M	0.6M	100.0%	13.8%	3.3M	2.6M	77.8%	2.0M	61.7%	0.5M	0.6M	13.9%	60.7%	53.0%	151bp	151bp	27%	7.7M	86.5%	330.2Mb	3.8M	42.5%	49.1%	61.9%	141.0bp	80.7%	42.0%	100bp	117bp	27%	3.8M
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	0.85	0.3M	0.1M	0.1M	0.0M	0.0M	0.65%	0.3M	0.3M	100.0%	0.0%	8.9%	0.3M	0.0bp	0.6M	0.6M	100.0%	15.2%	3.1M	2.7M	86.9%	2.2M	71.8%	0.5M	0.6M	14.2%	64.3%	51.0%	151bp	151bp	27%	5.9M	89.0%	339.4Mb	3.6M	42.5%	60.6%	55.6%	141.0bp	83.6%	42.0%	106bp	137bp	18%	3.6M
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	1.15	0.4M	0.1M	0.1M	0.0M	0.0M	0.61%	0.3M	0.4M	100.0%	0.0%	7.6%	0.4M	0.0bp	0.7M	0.7M	100.0%	15.1%	4.7M	4.2M	89.4%	3.5M	75.8%	0.6M	0.7M	11.8%	67.7%	48.0%	151bp	151bp	27%	8.6M	88.7%	536.6Mb	5.5M	41.4%	64.0%	50.6%	141.0bp	84.9%	41.0%	110bp	141bp	18%	5.5M
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	0.94	0.3M	0.1M	0.1M	0.0M	0.0M	0.64%	0.4M	0.3M	100.0%	0.0%	9.3%	0.3M	0.0bp	0.7M	0.7M	100.0%	14.6%	3.7M	3.0M	82.0%	2.5M	67.4%	0.5M	0.7M	15.4%	61.0%	52.0%	151bp	151bp	27%	7.9M	87.0%	394.6Mb	4.3M	42.4%	54.3%	57.4%	141.0bp	80.5%	42.0%	105bp	132bp	18%	4.3M
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	1.10	0.5M	0.2M	0.1M	0.1M	0.0M	0.58%	0.4M	0.5M	100.0%	0.0%	6.5%	0.5M	0.0bp	0.8M	0.8M	100.0%	15.5%	3.6M	3.2M	88.7%	2.6M	73.6%	0.5M	0.8M	18.7%	60.1%	49.0%	151bp	151bp	27%	7.1M	88.3%	411.9Mb	4.2M	41.7%	59.6%	52.0%	141.0bp	78.9%	41.0%	110bp	141bp	18%	4.2M
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	1.13	0.2M	0.0M	0.0M	0.0M	0.0M	0.79%	0.4M	0.2M	100.0%	0.0%	15.9%	0.2M	0.0bp	0.6M	0.6M	100.0%	14.9%	2.9M	2.1M	72.7%	1.5M	52.3%	0.6M	0.6M	14.1%	60.0%	54.0%	151bp	151bp	36%	9.1M	88.0%	268.4Mb	3.4M	43.3%	37.4%	71.6%	141.0bp	81.4%	43.0%	90bp	87bp	27%	3.4M
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	0.91	0.3M	0.1M	0.1M	0.0M	0.0M	0.79%	0.4M	0.3M	100.0%	0.0%	14.6%	0.3M	0.0bp	0.7M	0.7M	100.0%	12.6%	3.4M	2.6M	73.9%	1.9M	54.5%	0.7M	0.7M	15.5%	58.7%	53.0%	151bp	151bp	36%	9.5M	87.2%	317.7Mb	3.9M	43.1%	41.5%	68.8%	141.0bp	79.3%	43.0%	92bp	92bp	27%	3.9M
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	1.34	0.2M	0.0M	0.0M	0.0M	0.0M	0.78%	0.3M	0.2M	100.0%	0.0%	14.7%	0.2M	0.0bp	0.5M	0.5M	100.0%	15.6%	2.7M	2.0M	74.9%	1.6M	57.9%	0.5M	0.5M	14.2%	59.9%	53.0%	151bp	151bp	27%	7.1M	87.8%	270.4Mb	3.2M	42.3%	45.3%	63.8%	141.0bp	81.9%	42.0%	96bp	112bp	27%	3.2M
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	1.30	0.2M	0.1M	0.1M	0.0M	0.0M	0.68%	0.3M	0.2M	100.0%	0.0%	11.8%	0.2M	0.0bp	0.6M	0.6M	100.0%	14.0%	3.7M	3.1M	84.4%	2.5M	68.5%	0.6M	0.6M	11.4%	66.5%	49.0%	151bp	151bp	27%	7.5M	89.9%	401.2Mb	4.3M	42.5%	57.2%	57.8%	141.0bp	86.2%	42.0%	104bp	137bp	18%	4.3M
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	1.36	0.3M	0.1M	0.1M	0.0M	0.0M	0.75%	0.5M	0.3M	100.0%	0.0%	14.5%	0.3M	0.0bp	0.8M	0.8M	100.0%	13.9%	3.6M	2.8M	76.5%	2.1M	57.7%	0.7M	0.8M	15.9%	60.2%	54.0%	151bp	151bp	27%	9.3M	89.0%	341.4Mb	4.2M	43.4%	45.5%	69.4%	141.0bp	81.7%	43.0%	91bp	92bp	18%	4.2M
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	1.38	0.2M	0.1M	0.0M	0.0M	0.0M	0.78%	0.3M	0.2M	100.0%	0.0%	12.6%	0.2M	0.0bp	0.5M	0.5M	100.0%	16.0%	2.5M	2.0M	79.4%	1.5M	62.0%	0.4M	0.5M	14.9%	59.5%	52.0%	151bp	151bp	36%	6.2M	88.3%	257.3Mb	2.9M	42.5%	47.5%	63.1%	141.0bp	82.8%	42.0%	99bp	117bp	18%	2.9M
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	1.22	0.2M	0.0M	0.0M	0.0M	0.0M	0.86%	0.3M	0.2M	100.0%	0.0%	17.0%	0.2M	0.0bp	0.5M	0.5M	100.0%	12.0%	2.1M	1.3M	61.9%	0.9M	42.3%	0.4M	0.5M	18.9%	55.4%	53.0%	151bp	151bp	36%	7.2M	85.2%	165.1Mb	2.4M	41.0%	32.8%	72.6%	141.0bp	76.8%	41.0%	82bp	77bp	27%	2.4M
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	0.65	0.2M	0.0M	0.0M	0.0M	0.0M	1.03%	0.4M	0.2M	100.0%	0.0%	19.2%	0.2M	0.0bp	0.6M	0.6M	100.0%	6.1%	2.3M	1.4M	60.9%	0.9M	39.3%	0.5M	0.6M	20.1%	54.8%	56.0%	151bp	151bp	36%	9.1M	84.4%	155.5Mb	2.5M	41.9%	27.2%	78.5%	141.0bp	73.5%	41.0%	75bp	67bp	36%	2.5M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	0.99	0.2M	0.1M	0.0M	0.0M	0.0M	0.70%	0.3M	0.2M	100.0%	0.0%	12.7%	0.2M	0.0bp	0.5M	0.5M	100.0%	14.5%	3.0M	2.3M	77.7%	1.9M	62.3%	0.5M	0.5M	12.7%	61.5%	52.0%	151bp	151bp	36%	7.5M	87.8%	314.1Mb	3.5M	42.1%	46.7%	62.3%	141.0bp	82.9%	42.0%	102bp	122bp	27%	3.5M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	0.88	0.2M	0.0M	0.0M	0.0M	0.0M	0.81%	0.3M	0.2M	100.0%	0.0%	14.9%	0.2M	0.0bp	0.5M	0.5M	100.0%	12.8%	2.3M	1.7M	73.5%	1.3M	55.3%	0.4M	0.5M	17.4%	56.0%	54.0%	151bp	151bp	36%	6.6M	87.9%	217.9Mb	2.6M	42.8%	39.9%	67.8%	141.0bp	80.0%	42.0%	94bp	107bp	27%	2.6M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	1.14	0.1M	0.0M	0.0M	0.0M	0.0M	0.73%	0.2M	0.1M	100.0%	0.0%	14.7%	0.1M	0.0bp	0.4M	0.4M	100.0%	13.7%	2.1M	1.6M	76.8%	1.3M	59.7%	0.4M	0.4M	14.0%	59.7%	53.0%	151bp	151bp	36%	5.6M	88.3%	213.8Mb	2.4M	42.5%	43.4%	65.5%	141.0bp	82.4%	42.0%	99bp	117bp	18%	2.4M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	1.02	0.2M	0.0M	0.0M	0.0M	0.0M	0.76%	0.3M	0.2M	100.0%	0.0%	14.8%	0.2M	0.0bp	0.5M	0.5M	100.0%	13.6%	3.1M	2.3M	75.5%	1.8M	59.0%	0.5M	0.5M	12.5%	61.2%	53.0%	151bp	151bp	36%	8.4M	88.2%	309.7Mb	3.5M	42.6%	42.2%	64.9%	141.0bp	84.1%	42.0%	99bp	117bp	18%	3.5M
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	1.07	0.2M	0.1M	0.0M	0.0M	0.0M	0.71%	0.3M	0.2M	100.0%	0.0%	13.4%	0.2M	0.0bp	0.5M	0.5M	100.0%	14.7%	2.7M	2.1M	78.9%	1.7M	61.8%	0.5M	0.5M	14.3%	60.6%	52.0%	151bp	151bp	36%	6.8M	88.9%	282.8Mb	3.2M	42.8%	46.5%	64.5%	141.0bp	83.4%	42.0%	101bp	122bp	18%	3.2M
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	0.97	0.2M	0.1M	0.0M	0.0M	0.0M	0.68%	0.3M	0.2M	100.0%	0.0%	12.8%	0.2M	0.0bp	0.6M	0.6M	100.0%	14.1%	3.6M	2.9M	79.7%	2.3M	63.5%	0.6M	0.6M	12.6%	61.3%	53.0%	151bp	151bp	27%	8.9M	88.3%	372.4Mb	4.2M	42.9%	46.8%	63.9%	141.0bp	83.3%	42.0%	101bp	122bp	18%	4.2M
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	1.08	0.2M	0.0M	0.0M	0.0M	0.0M	0.77%	0.3M	0.2M	100.0%	0.0%	14.9%	0.2M	0.0bp	0.5M	0.5M	100.0%	13.3%	2.3M	1.7M	71.4%	1.3M	54.4%	0.4M	0.5M	16.1%	57.0%	54.0%	151bp	151bp	27%	7.0M	87.0%	227.5Mb	2.7M	42.2%	38.4%	66.0%	141.0bp	79.5%	42.0%	97bp	112bp	27%	2.7M
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	1.09	0.4M	0.2M	0.1M	0.1M	0.0M	0.58%	0.4M	0.4M	100.0%	0.0%	7.2%	0.4M	0.0bp	0.8M	0.8M	100.0%	13.6%	4.4M	3.9M	89.2%	3.3M	74.4%	0.7M	0.8M	14.1%	64.0%	48.0%	151bp	151bp	27%	8.6M	89.8%	512.7Mb	5.1M	42.1%	59.5%	51.2%	141.0bp	83.3%	42.0%	112bp	141bp	18%	5.1M
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	1.70	0.2M	0.0M	0.1M	0.0M	0.0M	0.74%	0.3M	0.2M	100.0%	0.0%	13.5%	0.2M	0.0bp	0.5M	0.5M	100.0%	10.3%	2.2M	1.7M	76.7%	1.3M	59.2%	0.4M	0.5M	17.7%	58.0%	52.0%	151bp	151bp	36%	5.5M	87.4%	211.7Mb	2.5M	41.2%	45.1%	64.0%	141.0bp	79.2%	41.0%	97bp	117bp	18%	2.5M
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	0.73	0.7M	0.3M	0.2M	0.1M	0.1M	0.56%	0.5M	0.7M	100.0%	0.0%	6.2%	0.7M	0.0bp	1.2M	1.2M	100.0%	17.3%	5.4M	5.0M	92.2%	4.2M	77.4%	0.8M	1.2M	17.1%	67.9%	44.0%	151bp	151bp	27%	8.5M	89.4%	661.8Mb	6.5M	41.1%	76.5%	40.9%	141.0bp	82.1%	41.0%	113bp	141bp	27%	6.5M
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	0.90	1.0M	0.5M	0.3M	0.1M	0.1M	0.52%	0.5M	1.0M	100.0%	0.0%	4.2%	1.0M	0.0bp	1.5M	1.5M	100.0%	12.3%	5.2M	5.0M	96.5%	4.1M	80.2%	0.8M	1.5M	22.1%	65.0%	42.0%	151bp	151bp	36%	6.8M	89.7%	613.5Mb	5.9M	41.0%	86.4%	34.1%	141.0bp	77.0%	40.0%	116bp	141bp	18%	5.9M
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	0.97	0.6M	0.3M	0.2M	0.0M	0.1M	0.53%	0.4M	0.6M	100.0%	0.0%	5.2%	0.6M	0.0bp	1.0M	1.0M	100.0%	15.8%	4.1M	3.9M	93.9%	3.4M	81.0%	0.5M	1.0M	18.2%	69.1%	43.0%	151bp	151bp	36%	5.9M	89.7%	516.0Mb	4.9M	41.2%	83.2%	34.4%	141.0bp	81.1%	41.0%	117bp	141bp	27%	4.9M
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	1.00	0.5M	0.2M	0.1M	0.0M	0.0M	0.55%	0.4M	0.5M	100.0%	0.0%	6.2%	0.5M	0.0bp	0.9M	0.9M	100.0%	16.2%	4.4M	4.1M	93.3%	3.5M	78.1%	0.7M	0.9M	14.7%	70.3%	45.0%	151bp	151bp	27%	6.9M	89.5%	543.3Mb	5.3M	41.8%	76.8%	39.3%	141.0bp	84.4%	41.0%	114bp	141bp	27%	5.3M
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	1.08	0.3M	0.1M	0.1M	0.0M	0.0M	0.68%	0.4M	0.3M	100.0%	0.0%	12.3%	0.3M	0.0bp	0.6M	0.6M	100.0%	11.6%	2.8M	2.2M	77.9%	1.7M	61.1%	0.5M	0.6M	18.0%	56.4%	52.0%	151bp	151bp	36%	6.6M	85.4%	275.5Mb	3.1M	41.2%	47.4%	58.0%	141.0bp	76.6%	41.0%	103bp	127bp	18%	3.1M
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	1.08	0.5M	0.2M	0.1M	0.0M	0.0M	0.53%	0.4M	0.5M	100.0%	0.0%	6.5%	0.5M	0.0bp	1.0M	1.0M	100.0%	17.5%	4.0M	3.7M	92.1%	3.0M	76.4%	0.6M	1.0M	18.2%	65.2%	45.0%	151bp	151bp	27%	6.6M	89.3%	476.7Mb	4.8M	41.3%	73.2%	44.2%	141.0bp	81.2%	41.0%	111bp	141bp	27%	4.8M
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	0.74	1.3M	0.6M	0.4M	0.1M	0.1M	0.50%	0.5M	1.3M	100.0%	0.0%	3.3%	1.3M	0.0bp	1.8M	1.8M	100.0%	22.9%	5.0M	4.8M	96.5%	4.1M	80.8%	0.8M	1.8M	28.1%	57.8%	41.0%	151bp	151bp	27%	7.6M	89.1%	645.1Mb	6.5M	40.2%	85.1%	38.9%	141.0bp	74.4%	40.0%	111bp	141bp	36%	6.5M
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	1.31	0.5M	0.2M	0.1M	0.0M	0.0M	0.58%	0.4M	0.5M	100.0%	0.0%	8.5%	0.5M	0.0bp	0.9M	0.9M	100.0%	13.8%	4.2M	3.5M	83.8%	2.9M	68.0%	0.7M	0.9M	16.4%	60.1%	52.0%	151bp	151bp	27%	10.2M	88.3%	447.4Mb	4.9M	42.4%	48.2%	62.2%	141.0bp	79.6%	42.0%	103bp	132bp	18%	4.9M
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	2.27	0.2M	0.0M	0.0M	0.0M	0.0M	0.83%	0.4M	0.2M	100.0%	0.0%	17.1%	0.2M	0.0bp	0.6M	0.6M	100.0%	14.5%	2.0M	1.3M	65.6%	0.9M	44.2%	0.4M	0.6M	21.0%	52.1%	56.0%	151bp	151bp	36%	7.2M	83.7%	167.8Mb	2.4M	42.2%	33.3%	72.8%	141.0bp	73.7%	42.0%	84bp	82bp	27%	2.4M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	0.79	0.6M	0.2M	0.2M	0.0M	0.1M	0.55%	0.4M	0.6M	100.0%	0.0%	5.7%	0.6M	0.0bp	1.0M	1.0M	100.0%	9.8%	6.2M	5.8M	93.3%	4.9M	78.7%	0.9M	1.0M	12.2%	72.3%	46.0%	151bp	151bp	27%	9.0M	90.0%	718.7Mb	6.9M	42.1%	77.0%	40.7%	141.0bp	85.0%	42.0%	116bp	141bp	18%	6.9M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	0.90	0.7M	0.3M	0.2M	0.1M	0.1M	0.54%	0.5M	0.7M	100.0%	0.0%	5.8%	0.7M	0.0bp	1.2M	1.2M	100.0%	10.4%	6.5M	6.1M	93.6%	5.2M	79.6%	0.9M	1.2M	13.9%	70.0%	45.0%	151bp	151bp	27%	9.5M	89.9%	749.7Mb	7.3M	41.5%	76.5%	41.4%	141.0bp	84.0%	41.0%	115bp	141bp	18%	7.3M
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	1.29	0.6M	0.2M	0.2M	0.0M	0.0M	0.56%	0.4M	0.6M	100.0%	0.0%	5.7%	0.6M	0.0bp	1.0M	1.0M	100.0%	14.2%	4.5M	4.2M	93.4%	3.6M	78.7%	0.7M	1.0M	16.8%	66.5%	44.0%	151bp	151bp	27%	7.2M	89.9%	532.1Mb	5.3M	41.5%	73.4%	45.6%	141.0bp	82.1%	41.0%	112bp	141bp	27%	5.3M
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	0.90	0.6M	0.3M	0.2M	0.1M	0.1M	0.56%	0.4M	0.6M	100.0%	0.0%	5.3%	0.6M	0.0bp	1.0M	1.0M	100.0%	13.2%	4.8M	4.5M	93.3%	3.9M	80.3%	0.6M	1.0M	16.6%	68.2%	44.0%	151bp	151bp	27%	7.2M	89.5%	571.0Mb	5.5M	41.1%	76.7%	39.5%	141.0bp	81.9%	41.0%	115bp	141bp	18%	5.5M
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	0.75	0.7M	0.3M	0.2M	0.1M	0.1M	0.54%	0.4M	0.7M	100.0%	0.0%	5.3%	0.7M	0.0bp	1.1M	1.1M	100.0%	15.8%	4.2M	3.9M	93.3%	3.3M	79.2%	0.6M	1.1M	20.5%	63.0%	45.0%	151bp	151bp	27%	6.8M	89.4%	495.2Mb	5.0M	41.6%	73.0%	45.9%	141.0bp	79.2%	41.0%	111bp	141bp	27%	5.0M
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	0.75	0.5M	0.2M	0.1M	0.0M	0.0M	0.54%	0.4M	0.5M	100.0%	0.0%	7.7%	0.5M	0.0bp	0.9M	0.9M	100.0%	11.1%	4.3M	3.7M	86.8%	3.1M	71.2%	0.7M	0.9M	16.9%	61.0%	49.0%	151bp	151bp	27%	8.6M	88.7%	476.9Mb	4.8M	41.1%	56.2%	51.6%	141.0bp	80.0%	41.0%	111bp	141bp	18%	4.8M
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	1.20	0.2M	0.1M	0.0M	0.0M	0.0M	0.55%	0.2M	0.2M	100.0%	0.0%	6.6%	0.2M	0.0bp	0.4M	0.4M	100.0%	12.6%	3.4M	3.2M	94.1%	2.7M	78.7%	0.5M	0.4M	8.8%	78.2%	44.0%	151bp	151bp	27%	5.0M	91.0%	421.8Mb	3.9M	42.7%	78.4%	31.5%	141.0bp	89.5%	42.0%	119bp	141bp	18%	3.9M
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	0.89	0.6M	0.3M	0.2M	0.1M	0.1M	0.55%	0.4M	0.6M	100.0%	0.0%	5.2%	0.6M	0.0bp	1.0M	1.0M	100.0%	17.9%	5.1M	4.9M	95.3%	4.1M	81.1%	0.7M	1.0M	14.9%	72.7%	43.0%	151bp	151bp	27%	7.5M	90.6%	653.2Mb	6.2M	42.2%	83.5%	35.1%	141.0bp	84.9%	42.0%	116bp	141bp	27%	6.2M
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	0.70	0.4M	0.2M	0.1M	0.0M	0.1M	0.52%	0.3M	0.4M	100.0%	0.0%	5.2%	0.4M	0.0bp	0.7M	0.7M	100.0%	16.4%	5.6M	5.4M	96.2%	4.5M	80.2%	0.9M	0.7M	9.7%	81.4%	41.0%	151bp	151bp	27%	7.5M	90.9%	739.9Mb	6.7M	42.2%	89.6%	24.5%	141.0bp	89.4%	42.0%	121bp	141bp	27%	6.7M
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	1.22	0.3M	0.1M	0.1M	0.0M	0.0M	0.54%	0.2M	0.3M	100.0%	0.0%	5.5%	0.3M	0.0bp	0.5M	0.5M	100.0%	14.5%	4.0M	3.8M	95.9%	3.3M	82.7%	0.5M	0.5M	9.9%	80.2%	42.0%	151bp	151bp	27%	5.4M	91.5%	507.6Mb	4.6M	42.1%	86.1%	30.5%	141.0bp	89.1%	42.0%	120bp	141bp	27%	4.6M
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	1.10	0.3M	0.2M	0.1M	0.0M	0.0M	0.52%	0.2M	0.3M	100.0%	0.0%	5.9%	0.3M	0.0bp	0.5M	0.5M	100.0%	17.9%	3.8M	3.6M	95.3%	3.0M	80.4%	0.6M	0.5M	10.3%	78.6%	42.0%	151bp	151bp	27%	5.4M	90.5%	494.8Mb	4.6M	42.1%	85.0%	28.3%	141.0bp	88.7%	42.0%	119bp	141bp	27%	4.6M
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	0.92	0.3M	0.2M	0.1M	0.0M	0.0M	0.57%	0.3M	0.3M	100.0%	0.0%	6.8%	0.3M	0.0bp	0.6M	0.6M	100.0%	14.6%	3.9M	3.6M	92.8%	3.1M	77.9%	0.6M	0.6M	12.1%	73.6%	45.0%	151bp	151bp	27%	5.8M	90.4%	488.9Mb	4.6M	42.6%	79.5%	34.1%	141.0bp	86.1%	42.0%	118bp	141bp	18%	4.6M
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	0.96	0.5M	0.2M	0.1M	0.0M	0.0M	0.52%	0.5M	0.5M	100.0%	0.0%	8.2%	0.5M	0.0bp	0.9M	0.9M	100.0%	21.2%	3.9M	3.5M	88.8%	2.8M	71.9%	0.7M	0.9M	18.0%	63.8%	49.0%	151bp	151bp	27%	7.3M	89.8%	476.2Mb	4.9M	43.0%	67.2%	48.9%	141.0bp	81.8%	43.0%	108bp	141bp	27%	4.9M
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	1.25	0.3M	0.1M	0.1M	0.0M	0.0M	0.55%	0.2M	0.3M	100.0%	0.0%	6.1%	0.3M	0.0bp	0.5M	0.5M	100.0%	13.7%	3.0M	2.8M	92.4%	2.3M	77.3%	0.5M	0.5M	13.9%	68.0%	48.0%	151bp	151bp	27%	5.1M	90.9%	360.4Mb	3.5M	42.7%	69.2%	46.5%	141.0bp	85.0%	42.0%	113bp	141bp	18%	3.5M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	0.99	0.4M	0.2M	0.1M	0.0M	0.0M	0.56%	0.4M	0.4M	100.0%	0.0%	8.3%	0.4M	0.0bp	0.8M	0.8M	100.0%	19.3%	4.5M	4.0M	89.3%	3.3M	74.1%	0.7M	0.8M	13.1%	68.2%	48.0%	151bp	151bp	27%	8.5M	90.1%	551.7Mb	5.6M	42.7%	65.9%	50.2%	141.0bp	85.6%	42.0%	110bp	141bp	27%	5.6M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	0.88	0.5M	0.2M	0.1M	0.0M	0.1M	0.54%	0.4M	0.5M	100.0%	0.0%	5.7%	0.5M	0.0bp	0.9M	0.9M	100.0%	15.9%	5.6M	5.3M	94.8%	4.5M	81.5%	0.7M	0.9M	12.7%	74.3%	44.0%	151bp	151bp	27%	8.2M	91.1%	702.2Mb	6.6M	42.3%	80.8%	37.4%	141.0bp	86.8%	42.0%	116bp	141bp	27%	6.6M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	0.92	0.4M	0.2M	0.1M	0.0M	0.0M	0.56%	0.3M	0.4M	100.0%	0.0%	6.0%	0.4M	0.0bp	0.6M	0.6M	100.0%	11.0%	5.5M	5.2M	94.6%	4.4M	80.3%	0.8M	0.6M	9.0%	78.9%	43.0%	151bp	151bp	27%	7.5M	91.3%	686.7Mb	6.2M	42.3%	82.6%	31.5%	141.0bp	89.4%	42.0%	121bp	141bp	18%	6.2M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	1.13	0.4M	0.2M	0.1M	0.0M	0.0M	0.55%	0.3M	0.4M	100.0%	0.0%	7.1%	0.4M	0.0bp	0.6M	0.6M	100.0%	11.1%	5.0M	4.6M	92.6%	3.9M	78.3%	0.7M	0.6M	10.0%	74.5%	46.0%	151bp	151bp	27%	7.4M	91.0%	602.6Mb	5.6M	43.2%	75.7%	39.0%	141.0bp	87.8%	43.0%	118bp	141bp	18%	5.6M
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	0.92	0.4M	0.1M	0.1M	0.0M	0.0M	0.58%	0.3M	0.4M	100.0%	0.0%	8.4%	0.4M	0.0bp	0.7M	0.7M	100.0%	10.6%	4.3M	3.8M	89.7%	3.2M	74.1%	0.7M	0.7M	12.6%	67.5%	47.0%	151bp	151bp	27%	7.2M	90.8%	493.3Mb	4.8M	42.7%	66.3%	46.0%	141.0bp	85.2%	42.0%	114bp	141bp	18%	4.8M
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	1.16	0.4M	0.2M	0.1M	0.0M	0.0M	0.58%	0.3M	0.4M	100.0%	0.0%	6.0%	0.4M	0.0bp	0.6M	0.6M	100.0%	11.7%	5.2M	4.9M	93.9%	4.2M	80.9%	0.7M	0.6M	9.6%	76.5%	44.0%	151bp	151bp	27%	7.5M	91.1%	632.3Mb	5.9M	42.3%	78.1%	34.3%	141.0bp	88.5%	42.0%	119bp	141bp	18%	5.9M
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	0.71	1.7M	0.8M	0.5M	0.1M	0.2M	0.47%	0.7M	1.7M	100.0%	0.0%	3.6%	1.7M	0.0bp	2.4M	2.4M	100.0%	14.6%	8.4M	8.2M	97.3%	7.1M	84.1%	1.1M	2.4M	22.3%	66.1%	41.0%	151bp	151bp	27%	11.0M	91.1%	1055.1Mb	9.9M	41.8%	89.4%	31.5%	141.0bp	78.3%	41.0%	118bp	141bp	27%	9.9M
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	2.54	0.2M	0.0M	0.0M	0.0M	0.0M	0.93%	0.5M	0.2M	100.0%	0.0%	19.1%	0.2M	0.0bp	0.7M	0.7M	100.0%	7.1%	2.2M	1.2M	54.2%	0.7M	32.2%	0.5M	0.7M	27.3%	50.9%	58.0%	151bp	151bp	36%	9.9M	82.9%	147.2Mb	2.4M	41.9%	24.0%	77.5%	141.0bp	68.5%	41.0%	75bp	67bp	36%	2.4M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	QualiMap: RNASeq	5'-3' bias	5'-3' bias	`qualimap_rnaseq-5_3_bias`
\|\|	QualiMap: RNASeq	M Aligned	Reads Aligned (millions)	`qualimap_rnaseq-reads_aligned`	read_count
\|\|	QualiMap: RNASeq	Exonic	Reads aligned to exonic regions	`qualimap_rnaseq-reads_aligned_exonic`	read_count
\|\|	QualiMap: RNASeq	Intronic	Reads aligned to intronic regions	`qualimap_rnaseq-reads_aligned_intronic`	read_count
\|\|	QualiMap: RNASeq	Intergenic	Reads aligned to intergenic regions	`qualimap_rnaseq-reads_aligned_intergenic`	read_count
\|\|	QualiMap: RNASeq	Overlapping Exon	Reads aligned to overlapping exon regions	`qualimap_rnaseq-reads_aligned_overlapping_exon`	read_count
\|\|	Samtools: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_stats-error_rate`
\|\|	Samtools: stats	Non-primary	Non-primary alignments (millions)	`samtools_stats-non_primary_alignments`	read_count
\|\|	Samtools: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_stats-reads_mapped`	read_count
\|\|	Samtools: stats	% Mapped	% Mapped reads	`samtools_stats-reads_mapped_percent`
\|\|	Samtools: stats	% Proper pairs	% Properly paired reads	`samtools_stats-reads_properly_paired_percent`
\|\|	Samtools: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_stats-reads_MQ0_percent`
\|\|	Samtools: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_stats-raw_total_sequences`	read_count
\|\|	Samtools: stats	Mean insert	Average insert size	`samtools_stats-insert_size_average`
\|\|	Samtools: flagstat	Reads	Total reads in the bam file (millions)	`samtools_flagstat-flagstat_total`	read_count
\|\|	Samtools: flagstat	Reads mapped	Reads mapped in the bam file (millions)	`samtools_flagstat-mapped_passed`	read_count
\|\|	Samtools: flagstat	% Reads mapped	% Reads mapped in the bam file	`samtools_flagstat-mapped_passed_pct`
\|\|	SortMeRNA	rRNA	Percentage of reads matched to a SortMeRNA database	`sortmerna-rRNA_pct`
\|\|	STAR	Total reads	Number of input reads	`star-total_reads`	read_count
\|\|	STAR	Aligned	Mapped reads	`star-mapped`	read_count
\|\|	STAR	Aligned	% Mapped reads	`star-mapped_percent`
\|\|	STAR	Uniq aligned	Uniquely mapped reads	`star-uniquely_mapped`	read_count
\|\|	STAR	Uniq aligned	% Uniquely mapped reads	`star-uniquely_mapped_percent`
\|\|	STAR	Multimapped	Multiple mapped reads	`star-multimapped`	read_count
\|\|	UMI-tools	M Unique Reads	Reads remaining after deduplication (millions)	`umi_tools-dedup_output_reads`	read_count
\|\|	UMI-tools	% Pass Dedup	% processed reads that passed deduplication	`umi_tools-dedup_percent_passing`
\|\|	FastQC (raw)	Dups	% duplicate reads	`fastqc_raw-percent_duplicates`
\|\|	FastQC (raw)	GC	Average % GC content	`fastqc_raw-percent_gc`
\|\|	FastQC (raw)	Avg len	Average read length	`fastqc_raw-avg_sequence_length`
\|\|	FastQC (raw)	Median len	Median read length	`fastqc_raw-median_sequence_length`
\|\|	FastQC (raw)	Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`fastqc_raw-percent_fails`
\|\|	FastQC (raw)	Seqs	Total sequences (millions)	`fastqc_raw-total_sequences`	read_count
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`fastp-after_filtering_q30_rate`
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`fastp-after_filtering_q30_bases`	base_count
\|\|	fastp	Reads After Filtering	Total reads after filtering (millions)	`fastp-filtering_result_passed_filter_reads`	read_count
\|\|	fastp	GC content	GC content after filtering	`fastp-after_filtering_gc_content`
\|\|	fastp	% PF	Percent reads passing filter	`fastp-pct_surviving`
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`fastp-pct_adapter`
\|\|	fastp	Mean R1 Length	Mean read length of R1	`fastp-before_filtering_read1_mean_length`
\|\|	FastQC (trimmed)	Dups	% duplicate reads	`fastqc_trimmed-percent_duplicates`
\|\|	FastQC (trimmed)	GC	Average % GC content	`fastqc_trimmed-percent_gc`
\|\|	FastQC (trimmed)	Avg len	Average read length	`fastqc_trimmed-avg_sequence_length`
\|\|	FastQC (trimmed)	Median len	Median read length	`fastqc_trimmed-median_sequence_length`
\|\|	FastQC (trimmed)	Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`fastqc_trimmed-percent_fails`
\|\|	FastQC (trimmed)	Seqs	Total sequences (millions)	`fastqc_trimmed-total_sequences`	read_count

Sample status checks

Reports on sample strandedness status, and any failures in trimming or mapping.

Strandedness Checks

The strandedness used for analysis in this workflow can either be provided by the user or automatically inferred by Salmon using a sample of reads. In both cases, strandedness is verified at the end of the workflow using RSeQC's infer_experiment.py on genomic alignments. In this table, a pass indicates a match between the supplied strandedness (or that inferred by Salmon) and RSeQC results. A fail indicates a mismatch or 'undetermined' strandedness. 'Undetermined' strandedness can signal QC issues, including potential genomic DNA contamination.

Note: Rows are duplicated for an 'auto' setting to allow comparison of statistics between inference methods.

Showing ¹²⁸/₁₂₈ rows and ⁷/₇ columns.

Sample	Status	Strand inference method	Provided strandedness	Inferred strandedness	Sense (%)	Antisense (%)	Unstranded (%)
CTL_0_S2_P1_R2_93_HG03111_ESN	pass	RSeQC	auto	forward	86.7	4.1	9.2
CTL_0_S2_P1_R2_115_HG03162_ESN	pass	RSeQC	auto	forward	89.3	2.4	8.3
CTL_0_S2_P1_R2_166_HG03517_ESN	pass	RSeQC	auto	forward	85.8	3.2	11.1
CTL_0_S2_P1_R2_194_GM18505_YRI	pass	RSeQC	auto	forward	86.1	3.3	10.5
CTL_0_S2_P1_R2_197_GM18511_YRI	pass	RSeQC	auto	forward	86.3	5.2	8.5
CTL_0_S2_P1_R2_199_GM18517_YRI	pass	RSeQC	auto	forward	85.6	3.9	10.5
CTL_0_S2_P1_R2_201_GM18520_YRI	pass	RSeQC	auto	forward	84.9	6.5	8.6
CTL_0_S2_P1_R2_203_GM18523_YRI	pass	RSeQC	auto	forward	86.6	4.1	9.4
CTL_0_S2_P1_R2_212_GM18873_YRI	pass	RSeQC	auto	forward	86.7	4.8	8.5
CTL_0_S2_P1_R2_216_GM18878_YRI	fail	RSeQC	auto	undetermined	57.6	35.8	6.6
CTL_0_S2_P1_R2_220_GM18909_YRI	pass	RSeQC	auto	forward	85.8	3.7	10.5
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	pass	RSeQC	auto	forward	88.3	2.4	9.2
CTL_0_S2_P1_R2_228_GM18933_YRI	pass	RSeQC	auto	forward	87.7	3.2	9.1
CTL_0_S2_P1_R2_236_GM19095_YRI	pass	RSeQC	auto	forward	86.1	5.2	8.7
CTL_0_S2_P1_R2_239_GM19099_YRI	pass	RSeQC	auto	forward	84.5	6.9	8.5
CTL_0_S2_P1_R2_240_GM19102_YRI	pass	RSeQC	auto	forward	86.7	4.3	9.1
CTL_0_S2_P1_R3_93_HG03111_ESN	pass	RSeQC	auto	forward	86.9	4.1	9.0
CTL_0_S2_P1_R3_115_HG03162_ESN	pass	RSeQC	auto	forward	87.3	2.2	10.5
CTL_0_S2_P1_R3_166_HG03517_ESN	pass	RSeQC	auto	forward	85.5	3.3	11.1
CTL_0_S2_P1_R3_194_GM18505_YRI	pass	RSeQC	auto	forward	87.5	3.9	8.7
CTL_0_S2_P1_R3_197_GM18511_YRI	pass	RSeQC	auto	forward	85.4	4.5	10.1
CTL_0_S2_P1_R3_199_GM18517_YRI	pass	RSeQC	auto	forward	87.4	4.5	8.1
CTL_0_S2_P1_R3_201_GM18520_YRI	pass	RSeQC	auto	forward	89.2	2.3	8.5
CTL_0_S2_P1_R3_203_GM18523_YRI	pass	RSeQC	auto	forward	82.8	6.1	11.1
CTL_0_S2_P1_R3_212_GM18873_YRI	pass	RSeQC	auto	forward	87.6	3.9	8.5
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	pass	RSeQC	auto	forward	84.3	5.6	10.1
CTL_0_S2_P1_R3_220_GM18909_YRI	pass	RSeQC	auto	forward	84.2	6.9	8.8
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	fail	RSeQC	auto	unstranded	46.8	47.1	6.1
CTL_0_S2_P1_R3_228_GM18933_YRI	pass	RSeQC	auto	forward	85.4	5.7	8.9
CTL_0_S2_P1_R3_236_GM19095_YRI	pass	RSeQC	auto	forward	87.4	3.4	9.1
CTL_0_S2_P1_R3_239_GM19099_YRI	fail	RSeQC	auto	unstranded	47.3	46.1	6.6
CTL_0_S2_P1_R3_240_GM19102_YRI	pass	RSeQC	auto	forward	87.1	4.2	8.7
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	pass	RSeQC	auto	forward	83.9	6.7	9.4
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	pass	RSeQC	auto	forward	89.2	2.7	8.0
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	pass	RSeQC	auto	forward	86.6	3.8	9.6
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	pass	RSeQC	auto	forward	84.4	4.0	11.6
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	pass	RSeQC	auto	forward	83.8	4.8	11.4
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	pass	RSeQC	auto	forward	84.5	6.3	9.1
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	pass	RSeQC	auto	forward	84.2	4.6	11.2
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	pass	RSeQC	auto	forward	88.5	2.9	8.6
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	pass	RSeQC	auto	forward	87.1	3.3	9.6
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	pass	RSeQC	auto	forward	75.5	17.2	7.3
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	pass	RSeQC	auto	forward	85.2	3.4	11.4
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	pass	RSeQC	auto	forward	87.6	3.8	8.6
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	pass	RSeQC	auto	forward	87.5	3.8	8.7
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	pass	RSeQC	auto	forward	87.5	3.6	8.9
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	pass	RSeQC	auto	forward	88.1	3.2	8.7
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	pass	RSeQC	auto	forward	84.3	4.6	11.1
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	pass	RSeQC	auto	forward	85.6	2.8	11.6
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	pass	RSeQC	auto	forward	86.2	3.4	10.4
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	pass	RSeQC	auto	forward	85.3	3.4	11.3
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	pass	RSeQC	auto	forward	85.1	3.7	11.2
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	pass	RSeQC	auto	forward	84.0	7.3	8.8
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	pass	RSeQC	auto	forward	84.2	4.9	10.9
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	pass	RSeQC	auto	forward	86.4	3.6	9.9
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	pass	RSeQC	auto	forward	83.7	4.3	11.9
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	pass	RSeQC	auto	forward	87.3	2.9	9.8
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	pass	RSeQC	auto	forward	87.1	3.0	9.9
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	pass	RSeQC	auto	forward	87.9	2.5	9.6
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	pass	RSeQC	auto	forward	83.9	4.2	11.9
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	pass	RSeQC	auto	forward	86.6	3.3	10.1
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	pass	RSeQC	auto	forward	86.0	5.3	8.7
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	pass	RSeQC	auto	forward	85.6	3.7	10.7
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	pass	RSeQC	auto	forward	84.7	4.9	10.4
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	pass	RSeQC	auto	forward	81.3	11.2	7.4
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	pass	RSeQC	auto	forward	81.6	7.8	10.6
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	pass	RSeQC	auto	forward	76.5	17.1	6.4
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	pass	RSeQC	auto	forward	81.5	10.5	8.0
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	pass	RSeQC	auto	forward	84.1	8.4	7.5
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	pass	RSeQC	auto	forward	84.8	6.1	9.1
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	pass	RSeQC	auto	forward	81.7	9.7	8.6
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	pass	RSeQC	auto	forward	73.9	18.9	7.1
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	pass	RSeQC	auto	forward	81.0	12.5	6.5
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	pass	RSeQC	auto	forward	64.7	25.4	9.8
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	pass	RSeQC	auto	forward	80.8	11.5	7.6
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	pass	RSeQC	auto	forward	80.9	11.0	8.1
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	pass	RSeQC	auto	forward	83.8	8.7	7.5
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	pass	RSeQC	auto	forward	84.3	6.3	9.4
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	pass	RSeQC	auto	forward	84.3	7.8	7.9
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	pass	RSeQC	auto	forward	83.8	6.5	9.7
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	pass	RSeQC	auto	forward	75.6	17.1	7.3
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	pass	RSeQC	auto	forward	77.0	16.6	6.5
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	pass	RSeQC	auto	forward	78.7	14.7	6.5
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	pass	RSeQC	auto	forward	82.3	10.2	7.5
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	pass	RSeQC	auto	forward	79.1	13.6	7.3
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	pass	RSeQC	auto	forward	81.6	11.5	6.9
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	pass	RSeQC	auto	forward	72.0	19.2	8.9
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	pass	RSeQC	auto	forward	72.8	22.9	4.3
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	pass	RSeQC	auto	forward	81.7	11.7	6.5
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	pass	RSeQC	auto	forward	75.5	17.2	7.3
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	pass	RSeQC	auto	forward	78.9	13.6	7.5
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	pass	RSeQC	auto	forward	78.2	14.4	7.5
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	pass	RSeQC	auto	forward	79.6	13.1	7.4
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	pass	RSeQC	auto	forward	80.9	11.7	7.4
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	pass	RSeQC	auto	forward	77.4	15.2	7.3
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	pass	RSeQC	auto	forward	83.0	7.7	9.4
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	pass	RSeQC	auto	forward	77.4	12.7	9.8
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	pass	RSeQC	auto	forward	86.5	4.6	9.0
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	pass	RSeQC	auto	forward	86.7	3.4	10.0
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	pass	RSeQC	auto	forward	87.6	3.8	8.6
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	pass	RSeQC	auto	forward	84.1	4.1	11.8
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	pass	RSeQC	auto	forward	82.2	9.6	8.2
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	pass	RSeQC	auto	forward	86.7	4.4	8.9
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	pass	RSeQC	auto	forward	87.0	2.7	10.3
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	pass	RSeQC	auto	forward	83.1	5.8	11.0
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	pass	RSeQC	auto	forward	76.5	15.5	8.0
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	pass	RSeQC	auto	forward	87.2	4.2	8.6
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	pass	RSeQC	auto	forward	87.1	4.2	8.7
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	pass	RSeQC	auto	forward	87.2	4.4	8.4
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	pass	RSeQC	auto	forward	87.1	4.2	8.7
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	pass	RSeQC	auto	forward	87.1	4.1	8.8
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	pass	RSeQC	auto	forward	83.4	5.7	10.9
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	pass	RSeQC	auto	forward	87.8	3.3	8.8
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	pass	RSeQC	auto	forward	87.1	4.2	8.7
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	pass	RSeQC	auto	forward	85.6	3.0	11.4
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	pass	RSeQC	auto	forward	86.7	3.5	9.9
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	pass	RSeQC	auto	forward	87.7	3.0	9.3
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	pass	RSeQC	auto	forward	85.8	4.2	10.0
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	pass	RSeQC	auto	forward	83.4	5.1	11.5
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	pass	RSeQC	auto	forward	86.0	3.8	10.2
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	pass	RSeQC	auto	forward	83.5	5.5	10.9
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	pass	RSeQC	auto	forward	85.7	4.0	10.3
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	pass	RSeQC	auto	forward	84.9	3.9	11.2
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	pass	RSeQC	auto	forward	84.9	4.6	10.5
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	pass	RSeQC	auto	forward	85.0	5.3	9.7
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	pass	RSeQC	auto	forward	85.6	3.9	10.5
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	pass	RSeQC	auto	forward	89.2	3.1	7.7
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	pass	RSeQC	auto	forward	68.2	22.9	8.9

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: fail_strand_check_table_table

Sort	Column	Description	ID
\|\|	Status	Pass if the strandedness inferred by RSeQC matches that provided by the user or predicted by Salmon. Fail otherwise.	`samples_strandedness_check-Status`
\|\|	Strand inference method	Tool used to detect strandedness	`samples_strandedness_check-Strand_inference_method`
\|\|	Provided strandedness	User-provided strandedness	`samples_strandedness_check-Provided_strandedness`
\|\|	Inferred strandedness	Interred strandedness	`samples_strandedness_check-Inferred_strandedness`
\|\|	Sense (%)	Sense (%)	`samples_strandedness_check-Sense`
\|\|	Antisense (%)	Antisense (%)	`samples_strandedness_check-Antisense`
\|\|	Unstranded (%)	Unstranded (%)	`samples_strandedness_check-Unstranded`

FastQC (raw)

This section of the report shows FastQC results before adapter trimming.http://www.bioinformatics.babraham.ac.uk/projects/fastqc

Sequence Counts

Sequence counts for each sample. Duplicate read counts are an estimate only.

This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

Created with MultiQC

Sequence Quality Histograms

127

1

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

Created with MultiQC

Per Sequence Quality Scores

128

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

Created with MultiQC

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

To see the data as a line plot, as in the original FastQC graph, click on a sample track.

From the FastQC help:

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

$ Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

36

66

26

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

Created with MultiQC

Per Base N Content

128

The percentage of base calls at each position for which an N was called.

From the FastQC help:

If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

Created with MultiQC

Sequence Length Distribution

128

All samples have sequences of a single length (151bp)

Sequence Duplication Levels

2

126

The relative level of duplication found for every sequence.

From the FastQC Help:

In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

Created with MultiQC

Overrepresented sequences by sample

The total amount of overrepresented sequences found in each library.

FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

From the FastQC Help:

A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

128 samples had less than 1% of reads made up of overrepresented sequences

Top overrepresented sequences

Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

Showing ⁴/₄ rows and ³/₃ columns.

Overrepresented sequence	Reports	Occurrences	% of all reads
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	57	828434	0.0859%
AAAAATTATAACCAAGCATAACATAGCAAGGACTAACCCCTATACCTTCT	5	56964	0.0059%
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	3	32884	0.0034%
AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT	3	29415	0.0030%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: fastqc_raw_top_overrepresented_sequences_table_table

Sort	Column	Description	ID
\|\|	Reports	Number of FastQC reports where this sequence is founds as overrepresented	`fastqc_raw-samples`
\|\|	Occurrences	Total number of occurrences of the sequence (among the samples where the sequence is overrepresented)	`fastqc_raw-total_count`
\|\|	% of all reads	Total number of occurrences as the percentage of all reads (among samples where the sequence is overrepresented)	`fastqc_raw-total_percent`

Adapter Content

128

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

Created with MultiQC

Status Checks

Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

Created with MultiQC

fastp

All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

Filtered Reads

Filtering statistics of sampled reads.

Created with MultiQC

Sequence Quality

Average sequencing quality over each base of all reads.

Created with MultiQC

GC Content

Average GC content over each base of all reads.

Created with MultiQC

N content

Average N content over each base of all reads.

Created with MultiQC

FastQC (trimmed)

This section of the report shows FastQC results after adapter trimming.http://www.bioinformatics.babraham.ac.uk/projects/fastqc

Sequence Counts

Sequence counts for each sample. Duplicate read counts are an estimate only.

This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

Created with MultiQC

Sequence Quality Histograms

126

2

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

Created with MultiQC

Per Sequence Quality Scores

128

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

Created with MultiQC

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

To see the data as a line plot, as in the original FastQC graph, click on a sample track.

From the FastQC help:

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

$ Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

50

40

38

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

Created with MultiQC

Per Base N Content

128

The percentage of base calls at each position for which an N was called.

From the FastQC help:

If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

Created with MultiQC

Sequence Length Distribution

128

The distribution of fragment sizes (read lengths) found. See the FastQC help

Created with MultiQC

Sequence Duplication Levels

128

The relative level of duplication found for every sequence.

From the FastQC Help:

In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

Created with MultiQC

Overrepresented sequences by sample

The total amount of overrepresented sequences found in each library.

FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

From the FastQC Help:

A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

Created with MultiQC

Top overrepresented sequences

Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

Showing ²⁰/₂₀ rows and ³/₃ columns.

Overrepresented sequence	Reports	Occurrences	% of all reads
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	107	1713056	0.2705%
GCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	101	1502774	0.2373%
ACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAA	94	1042398	0.1646%
GCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAAC	93	983218	0.1553%
CCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAG	92	983139	0.1553%
GTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGG	82	718036	0.1134%
AGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	59	598576	0.0945%
ACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	44	392682	0.0620%
ACCAAGCATAACATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAA	24	385639	0.0609%
CTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATT	44	324664	0.0513%
GAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA	48	310443	0.0490%
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	39	304200	0.0480%
TCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	27	260297	0.0411%
ACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAAC	34	211743	0.0334%
GTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAACATAGCAAGG	21	198065	0.0313%
GGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAA	28	174809	0.0276%
GCTTTTCAGTCTCGACGGGCTAGCACACATCTGGTTGACTAGGCGCATAG	17	147371	0.0233%
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	17	141896	0.0224%
GGCTGGTGTTAGGGTTCTTTGTTTTTGGGGTTTGGCAGAGATGTGTTTAA	18	139111	0.0220%
GCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	17	138773	0.0219%

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: fastqc_trimmed_top_overrepresented_sequences_table_table

Sort	Column	Description	ID
\|\|	Reports	Number of FastQC reports where this sequence is founds as overrepresented	`fastqc_trimmed-samples`
\|\|	Occurrences	Total number of occurrences of the sequence (among the samples where the sequence is overrepresented)	`fastqc_trimmed-total_count`
\|\|	% of all reads	Total number of occurrences as the percentage of all reads (among samples where the sequence is overrepresented)	`fastqc_trimmed-total_percent`

Adapter Content

128

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

Created with MultiQC

Status Checks

Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

Created with MultiQC

Preseq

Estimates library complexity, showing how many additional unique reads are sequenced for increasing total read count.http://smithlabresearch.org/software/preseqDOI: 10.1038/nmeth.2375

A shallow curve indicates complexity saturation. The dashed line shows a perfectly complex library where total reads = unique reads.

Complexity curve (molecule count)

Note that the x-axis is trimmed at the point where all the datasets show 80% of their maximum y-value, to avoid ridiculous scales.

Created with MultiQC

QualiMap

Quality control of alignment data and its derivatives like feature counts.http://qualimap.bioinfo.cipf.esDOI: 10.1093/bioinformatics/btv566; 10.1093/bioinformatics/bts503

Genomic origin of reads

Classification of mapped reads as originating in exonic, intronic or intergenic regions. These can be displayed as either the number or percentage of mapped reads.

There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. This allows mapped reads to be grouped by whether they originate in an exonic region (for QualiMap, this may include 5′ and 3′ UTR regions as well as protein-coding exons), an intron, or an intergenic region (see the Qualimap 2 documentation).

The inferred genomic origins of RNA-seq reads are presented here as a bar graph showing either the number or percentage of mapped reads in each read dataset that have been assigned to each type of genomic region. This graph can be used to assess the proportion of useful reads in an RNA-seq experiment. That proportion can be reduced by the presence of intron sequences, especially if depletion of ribosomal RNA was used during sample preparation (Sims et al. 2014). It can also be reduced by off-target transcripts, which are detected in greater numbers at the sequencing depths needed to detect poorly-expressed transcripts (Tarazona et al. 2011).

Created with MultiQC

Gene Coverage Profile

Mean distribution of coverage depth across the length of all mapped transcripts.

There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. QualiMap uses this information to calculate the depth of coverage along the length of each annotated transcript. For a set of reads mapped to a transcript, the depth of coverage at a given base position is the number of high-quality reads that map to the transcript at that position (Sims et al. 2014).

QualiMap calculates coverage depth at every base position of each annotated transcript. To enable meaningful comparison between transcripts, base positions are rescaled to relative positions expressed as percentage distance along each transcript (0%, 1%, …, 99%). For the set of transcripts with at least one mapped read, QualiMap plots the cumulative mapped-read depth (y-axis) at each relative transcript position (x-axis). This plot shows the gene coverage profile across all mapped transcripts for each read dataset. It provides a visual way to assess positional biases, such as an accumulation of mapped reads at the 3′ end of transcripts, which may indicate poor RNA quality in the original sample (Conesa et al. 2016).

The Normalised plot is calculated by MultiQC to enable comparison of samples with varying sequencing depth. The cumulative mapped-read depth at each position across the averaged transcript position are divided by the total for that sample across the entire averaged transcript.

Created with MultiQC

RSeQC

Evaluates high throughput RNA-seq data.http://rseqc.sourceforge.netDOI: 10.1093/bioinformatics/bts356

Read Distribution

Read Distribution calculates how mapped reads are distributed over genome features.

Created with MultiQC

Read Duplication

read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.

Created with MultiQC

Junction Annotation

Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.

Created with MultiQC

Junction Saturation

Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.

Created with MultiQC

Infer experiment

Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

Created with MultiQC

Bam Stat

All numbers reported in millions.

Created with MultiQC

Showing ¹²⁸/₁₂₈ rows and ¹⁰/₁₀ columns.

Sample Name	Total records	QC failed	Duplicates	Non primary hit	Unmapped	Unique	+ve strand	-ve strand	Non-splice reads	Splice reads
CTL_0_S2_P1_R2_93_HG03111_ESN	1.1M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
CTL_0_S2_P1_R2_115_HG03162_ESN	2.5M	0.0M	0.0M	0.8M	0.0M	1.4M	0.8M	0.6M	1.2M	0.3M
CTL_0_S2_P1_R2_166_HG03517_ESN	0.7M	0.0M	0.0M	0.3M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
CTL_0_S2_P1_R2_194_GM18505_YRI	1.7M	0.0M	0.0M	0.6M	0.0M	0.9M	0.5M	0.4M	0.7M	0.1M
CTL_0_S2_P1_R2_197_GM18511_YRI	0.5M	0.0M	0.0M	0.2M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
CTL_0_S2_P1_R2_199_GM18517_YRI	0.8M	0.0M	0.0M	0.3M	0.0M	0.4M	0.2M	0.1M	0.3M	0.1M
CTL_0_S2_P1_R2_201_GM18520_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
CTL_0_S2_P1_R2_203_GM18523_YRI	1.3M	0.0M	0.0M	0.5M	0.0M	0.6M	0.3M	0.2M	0.5M	0.1M
CTL_0_S2_P1_R2_212_GM18873_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.4M	0.1M
CTL_0_S2_P1_R2_216_GM18878_YRI	0.4M	0.0M	0.0M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_220_GM18909_YRI	0.6M	0.0M	0.0M	0.2M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	2.1M	0.0M	0.0M	0.6M	0.0M	1.2M	0.7M	0.5M	1.0M	0.2M
CTL_0_S2_P1_R2_228_GM18933_YRI	1.1M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.5M	0.1M
CTL_0_S2_P1_R2_236_GM19095_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
CTL_0_S2_P1_R2_239_GM19099_YRI	0.7M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
CTL_0_S2_P1_R2_240_GM19102_YRI	1.2M	0.0M	0.0M	0.5M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
CTL_0_S2_P1_R3_93_HG03111_ESN	0.3M	0.0M	0.0M	0.1M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
CTL_0_S2_P1_R3_115_HG03162_ESN	1.8M	0.0M	0.0M	0.6M	0.0M	1.0M	0.6M	0.4M	0.8M	0.2M
CTL_0_S2_P1_R3_166_HG03517_ESN	0.7M	0.0M	0.0M	0.3M	0.0M	0.4M	0.2M	0.1M	0.3M	0.1M
CTL_0_S2_P1_R3_194_GM18505_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
CTL_0_S2_P1_R3_197_GM18511_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.3M	0.1M	0.1M	0.2M	0.0M
CTL_0_S2_P1_R3_199_GM18517_YRI	0.4M	0.0M	0.0M	0.2M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
CTL_0_S2_P1_R3_201_GM18520_YRI	2.3M	0.0M	0.0M	0.8M	0.0M	1.3M	0.7M	0.6M	1.0M	0.3M
CTL_0_S2_P1_R3_203_GM18523_YRI	0.7M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.2M	0.0M
CTL_0_S2_P1_R3_212_GM18873_YRI	0.8M	0.0M	0.0M	0.3M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	0.8M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
CTL_0_S2_P1_R3_220_GM18909_YRI	0.7M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	0.6M	0.0M	0.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_228_GM18933_YRI	0.7M	0.0M	0.0M	0.3M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
CTL_0_S2_P1_R3_236_GM19095_YRI	1.1M	0.0M	0.0M	0.4M	0.0M	0.6M	0.3M	0.3M	0.5M	0.1M
CTL_0_S2_P1_R3_239_GM19099_YRI	0.6M	0.0M	0.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_240_GM19102_YRI	1.4M	0.0M	0.0M	0.5M	0.0M	0.7M	0.4M	0.3M	0.6M	0.1M
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	0.7M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	2.4M	0.0M	0.0M	0.7M	0.0M	1.4M	0.8M	0.6M	1.2M	0.2M
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	0.9M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	0.9M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	0.8M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.3M	0.1M
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	0.7M	0.0M	0.0M	0.3M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	0.7M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.3M	0.0M
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	2.4M	0.0M	0.0M	0.7M	0.0M	1.4M	0.8M	0.6M	1.2M	0.2M
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	1.1M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.0M	0.0M	0.1M	0.0M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	0.6M	0.0M	0.0M	0.2M	0.0M	0.3M	0.2M	0.1M	0.3M	0.1M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	0.8M	0.0M	0.0M	0.3M	0.0M	0.4M	0.2M	0.2M	0.4M	0.1M
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	1.0M	0.0M	0.0M	0.3M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	0.9M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	0.6M	0.0M	0.0M	0.2M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	0.7M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	0.6M	0.0M	0.0M	0.2M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	0.8M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.3M	0.1M
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	0.5M	0.0M	0.0M	0.2M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	0.8M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	1.4M	0.0M	0.0M	0.5M	0.0M	0.7M	0.4M	0.3M	0.6M	0.1M
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	0.8M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	1.5M	0.0M	0.0M	0.4M	0.0M	0.9M	0.5M	0.4M	0.8M	0.1M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	1.1M	0.0M	0.0M	0.3M	0.0M	0.6M	0.3M	0.3M	0.5M	0.1M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	0.7M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.2M	0.3M	0.1M
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	1.5M	0.0M	0.0M	0.5M	0.0M	0.8M	0.5M	0.4M	0.7M	0.1M
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	0.4M	0.0M	0.0M	0.2M	0.0M	0.1M	0.1M	0.1M	0.1M	0.0M
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	0.7M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	0.8M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	0.6M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	1.1M	0.0M	0.0M	0.6M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	0.6M	0.0M	0.0M	0.4M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	0.6M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	0.7M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	0.6M	0.0M	0.0M	0.4M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	0.4M	0.0M	0.0M	0.3M	0.0M	0.1M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	0.6M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	0.7M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.2M	0.0M
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	0.7M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	0.8M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	0.6M	0.0M	0.0M	0.4M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	0.7M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	0.8M	0.0M	0.0M	0.5M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.0M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	0.6M	0.0M	0.0M	0.4M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	0.4M	0.0M	0.0M	0.2M	0.0M	0.1M	0.0M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.1M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	0.8M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.3M	0.0M
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	0.5M	0.0M	0.0M	0.3M	0.0M	0.1M	0.1M	0.1M	0.1M	0.0M
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	1.2M	0.0M	0.0M	0.5M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	1.5M	0.0M	0.0M	0.5M	0.0M	0.8M	0.5M	0.4M	0.7M	0.1M
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	0.9M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	0.6M	0.0M	0.0M	0.4M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.4M	0.1M
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	1.8M	0.0M	0.0M	0.5M	0.0M	1.1M	0.6M	0.5M	0.9M	0.2M
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	0.9M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.3M	0.1M
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	0.6M	0.0M	0.0M	0.4M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	1.2M	0.0M	0.0M	0.5M	0.0M	0.5M	0.3M	0.2M	0.5M	0.1M
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	1.1M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.5M	0.1M
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	0.9M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	0.4M	0.0M	0.0M	0.2M	0.0M	0.2M	0.1M	0.1M	0.1M	0.0M
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	1.0M	0.0M	0.0M	0.4M	0.0M	0.5M	0.3M	0.2M	0.4M	0.1M
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	0.7M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.3M	0.1M
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	0.5M	0.0M	0.0M	0.2M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	0.5M	0.0M	0.0M	0.2M	0.0M	0.2M	0.1M	0.1M	0.2M	0.1M
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.3M	0.1M	0.1M	0.2M	0.1M
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	0.9M	0.0M	0.0M	0.5M	0.0M	0.3M	0.2M	0.1M	0.3M	0.1M
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	0.5M	0.0M	0.0M	0.2M	0.0M	0.2M	0.1M	0.1M	0.2M	0.0M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	0.8M	0.0M	0.0M	0.4M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	0.9M	0.0M	0.0M	0.4M	0.0M	0.4M	0.2M	0.2M	0.3M	0.1M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.2M	0.1M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	0.6M	0.0M	0.0M	0.3M	0.0M	0.3M	0.1M	0.1M	0.2M	0.1M
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	0.7M	0.0M	0.0M	0.3M	0.0M	0.3M	0.1M	0.1M	0.2M	0.0M
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	0.6M	0.0M	0.0M	0.3M	0.0M	0.3M	0.2M	0.1M	0.2M	0.0M
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	2.4M	0.0M	0.0M	0.7M	0.0M	1.4M	0.8M	0.6M	1.2M	0.3M
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	0.7M	0.0M	0.0M	0.5M	0.0M	0.1M	0.1M	0.0M	0.1M	0.0M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: rseqc_bam_stat_table

Sort	Column	Description	ID	Scale
\|\|	Total records	Total records	`total_records`	read_count
\|\|	QC failed	QC failed	`qc_failed`	read_count
\|\|	Duplicates	Optical/PCR duplicate	`optical_pcr_duplicate`	read_count
\|\|	Non primary hit	Non primary hit	`non_primary_hits`	read_count
\|\|	Unmapped	Unmapped reads	`unmapped_reads`	read_count
\|\|	Unique	mapq >= mapq_cut (unique)	`mapq_gte_mapq_cut_unique`	read_count
\|\|	+ve strand	Reads map to '+'	`reads_map_to_sense`	read_count
\|\|	-ve strand	Reads map to '-'	`reads_map_to_antisense`	read_count
\|\|	Non-splice reads	Non-splice reads	`non_splice_reads`	read_count
\|\|	Splice reads	Splice reads	`splice_reads`	read_count

Samtools

Toolkit for interacting with BAM/CRAM files.http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Percent mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

Created with MultiQC

Alignment stats

This module parses the output from samtools stats. All numbers in millions.

Created with MultiQC

Showing ¹²⁸/₁₂₈ rows and ¹³/₁₃ columns.

Sample Name	Total sequences	Mapped & paired	Properly paired	Duplicated	QC Failed	Reads MQ0	Mapped bases (CIGAR)	Bases Trimmed	Duplicated bases	Diff chromosomes	Other orientation	Inward pairs	Outward pairs
CTL_0_S2_P1_R2_93_HG03111_ESN	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	61.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_115_HG03162_ESN	1.7M	0.0M	0.0M	0.0M	0.0M	0.1M	172.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_166_HG03517_ESN	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	45.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_194_GM18505_YRI	1.1M	0.0M	0.0M	0.0M	0.0M	0.1M	102.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_197_GM18511_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	22.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_199_GM18517_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	42.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_201_GM18520_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	18.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_203_GM18523_YRI	0.8M	0.0M	0.0M	0.0M	0.0M	0.0M	69.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_212_GM18873_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	49.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_216_GM18878_YRI	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	2.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_220_GM18909_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	33.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	1.4M	0.0M	0.0M	0.0M	0.0M	0.1M	140.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_228_GM18933_YRI	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	65.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_236_GM19095_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	26.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_239_GM19099_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	25.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_240_GM19102_YRI	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	63.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_93_HG03111_ESN	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	18.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_115_HG03162_ESN	1.2M	0.0M	0.0M	0.0M	0.0M	0.0M	121.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_166_HG03517_ESN	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	42.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_194_GM18505_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	54.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_197_GM18511_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	30.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_199_GM18517_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	18.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_201_GM18520_YRI	1.6M	0.0M	0.0M	0.0M	0.0M	0.1M	156.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_203_GM18523_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	28.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_212_GM18873_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	47.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	36.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_220_GM18909_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	25.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	2.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_228_GM18933_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	26.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_236_GM19095_YRI	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	68.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_239_GM19099_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	2.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_240_GM19102_YRI	0.8M	0.0M	0.0M	0.0M	0.0M	0.0M	77.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	24.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	1.7M	0.0M	0.0M	0.0M	0.0M	0.1M	168.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	47.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	44.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	39.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	26.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	35.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	1.6M	0.0M	0.0M	0.0M	0.0M	0.1M	162.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	63.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	6.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	37.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	57.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	61.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	49.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	57.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	41.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	37.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	36.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	33.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	39.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	17.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	35.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	0.9M	0.0M	0.0M	0.0M	0.0M	0.0M	88.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	43.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	59.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	1.1M	0.0M	0.0M	0.0M	0.0M	0.0M	110.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	75.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	40.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	1.0M	0.0M	0.0M	0.0M	0.0M	0.0M	98.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	17.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	35.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	34.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	13.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	42.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	10.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	15.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	18.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	50.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	13.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	7.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	10.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	3.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	13.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	13.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	20.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	29.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	25.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	41.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	9.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	14.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	9.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	15.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	15.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	11.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	6.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	5.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	11.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	8.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	7.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	8.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	11.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	13.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	9.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	35.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	11.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	62.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	1.0M	0.0M	0.0M	0.0M	0.0M	0.0M	97.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	55.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	45.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	16.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	47.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	1.3M	0.0M	0.0M	0.0M	0.0M	0.0M	128.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	35.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	8.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	53.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	62.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	52.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	56.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	62.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	41.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	20.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	57.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	42.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	28.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	28.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	30.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	40.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	27.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	32.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	49.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	34.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	31.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	29.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	33.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	1.7M	0.0M	0.0M	0.0M	0.0M	0.1M	169.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	8.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-stats-dp_table

Sort	Column	Description	ID	Scale
\|\|	Total sequences	Total sequences	`raw_total_sequences`	read_count
\|\|	Mapped & paired	Paired-end technology bit set + both mates mapped	`reads_mapped_and_paired`	read_count
\|\|	Properly paired	Proper-pair bit set	`reads_properly_paired`	read_count
\|\|	Duplicated	PCR or optical duplicate bit set	`reads_duplicated`	read_count
\|\|	QC Failed	QC Failed	`reads_QC_failed`	read_count
\|\|	Reads MQ0	Reads mapped and MQ=0	`reads_MQ0`	read_count
\|\|	Mapped bases (CIGAR)	Mapped bases (CIGAR)	`bases_mapped__cigar`	base_count
\|\|	Bases Trimmed	Bases Trimmed	`bases_trimmed`	base_count
\|\|	Duplicated bases	Duplicated bases	`bases_duplicated`	base_count
\|\|	Diff chromosomes	Pairs on different chromosomes	`pairs_on_different_chromosomes`	read_count
\|\|	Other orientation	Pairs with other orientation	`pairs_with_other_orientation`	read_count
\|\|	Inward pairs	Inward oriented pairs	`inward_oriented_pairs`	read_count
\|\|	Outward pairs	Outward oriented pairs	`outward_oriented_pairs`	read_count

Flagstat

This module parses the output from samtools flagstat

Created with MultiQC

Showing ¹²⁸/₁₂₈ rows and ¹¹/₁₁ columns.

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
CTL_0_S2_P1_R2_93_HG03111_ESN	1.1M	1.1M	1.1M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_115_HG03162_ESN	2.5M	2.5M	2.5M	0.8M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_166_HG03517_ESN	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_194_GM18505_YRI	1.7M	1.7M	1.7M	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_197_GM18511_YRI	0.5M	0.5M	0.5M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_199_GM18517_YRI	0.8M	0.8M	0.8M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_201_GM18520_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_203_GM18523_YRI	1.3M	1.3M	1.3M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_212_GM18873_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_216_GM18878_YRI	0.4M	0.4M	0.4M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_220_GM18909_YRI	0.6M	0.6M	0.6M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	2.1M	2.1M	2.1M	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_228_GM18933_YRI	1.1M	1.1M	1.1M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_236_GM19095_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_239_GM19099_YRI	0.7M	0.7M	0.7M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R2_240_GM19102_YRI	1.2M	1.2M	1.2M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_93_HG03111_ESN	0.3M	0.3M	0.3M	0.1M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_115_HG03162_ESN	1.8M	1.8M	1.8M	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_166_HG03517_ESN	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_194_GM18505_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_197_GM18511_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_199_GM18517_YRI	0.4M	0.4M	0.4M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_201_GM18520_YRI	2.3M	2.3M	2.3M	0.8M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_203_GM18523_YRI	0.7M	0.7M	0.7M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_212_GM18873_YRI	0.8M	0.8M	0.8M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_220_GM18909_YRI	0.7M	0.7M	0.7M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_228_GM18933_YRI	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_236_GM19095_YRI	1.1M	1.1M	1.1M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_239_GM19099_YRI	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
CTL_0_S2_P1_R3_240_GM19102_YRI	1.4M	1.4M	1.4M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	0.7M	0.7M	0.7M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	2.4M	2.4M	2.4M	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	0.9M	0.9M	0.9M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	0.9M	0.9M	0.9M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	2.4M	2.4M	2.4M	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	1.1M	1.1M	1.1M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	0.6M	0.6M	0.6M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	0.8M	0.8M	0.8M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	1.0M	1.0M	1.0M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	0.9M	0.9M	0.9M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	0.6M	0.6M	0.6M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	0.6M	0.6M	0.6M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	0.8M	0.8M	0.8M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	0.5M	0.5M	0.5M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	1.4M	1.4M	1.4M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	1.5M	1.5M	1.5M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	1.1M	1.1M	1.1M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	1.5M	1.5M	1.5M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	0.4M	0.4M	0.4M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	1.1M	1.1M	1.1M	0.6M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	0.7M	0.7M	0.7M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	0.4M	0.4M	0.4M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	0.7M	0.7M	0.7M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	0.7M	0.7M	0.7M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	0.8M	0.8M	0.8M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	0.4M	0.4M	0.4M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	0.5M	0.5M	0.5M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	1.2M	1.2M	1.2M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	1.5M	1.5M	1.5M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	0.9M	0.9M	0.9M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	1.8M	1.8M	1.8M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	0.9M	0.9M	0.9M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	0.6M	0.6M	0.6M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	1.2M	1.2M	1.2M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	1.1M	1.1M	1.1M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	0.9M	0.9M	0.9M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	0.4M	0.4M	0.4M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	1.0M	1.0M	1.0M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	0.5M	0.5M	0.5M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	0.5M	0.5M	0.5M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	0.9M	0.9M	0.9M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	0.5M	0.5M	0.5M	0.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	0.8M	0.8M	0.8M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	0.9M	0.9M	0.9M	0.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	0.7M	0.7M	0.7M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	0.6M	0.6M	0.6M	0.3M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	2.4M	2.4M	2.4M	0.7M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	0.7M	0.7M	0.7M	0.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-flagstat-table_table

Sort	Column	Description	ID	Scale
\|\|	Total Reads	Total Reads	`flagstat_total`	read_count
\|\|	Total Passed QC	Total Passed QC	`total_passed`	read_count
\|\|	Mapped	Mapped	`mapped_passed`	read_count
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed`	read_count
\|\|	Duplicates	Duplicates	`duplicates_passed`	read_count
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed`	read_count
\|\|	Properly Paired	Properly Paired	`properly_paired_passed`	read_count
\|\|	Self and mate mapped	Reads with itself and mate mapped	`with_itself_and_mate_mapped_passed`	read_count
\|\|	Singletons	Singletons	`singletons_passed`	read_count
\|\|	Mate mapped to diff chr	Mate mapped to different chromosome	`with_mate_mapped_to_a_different_chr_passed`	read_count
\|\|	Diff chr (mapQ >= 5)	Mate mapped to different chromosome (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed`	read_count

Flagstat: Percentage of total

This module parses the output from samtools flagstat

Created with MultiQC

Showing ¹²⁸/₁₂₈ rows and ¹¹/₁₁ columns.

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
CTL_0_S2_P1_R2_93_HG03111_ESN	100.0%	100.0%	100.0%	40.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_115_HG03162_ESN	100.0%	100.0%	100.0%	31.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_166_HG03517_ESN	100.0%	100.0%	100.0%	37.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_194_GM18505_YRI	100.0%	100.0%	100.0%	36.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_197_GM18511_YRI	100.0%	100.0%	100.0%	48.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_199_GM18517_YRI	100.0%	100.0%	100.0%	41.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_201_GM18520_YRI	100.0%	100.0%	100.0%	52.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_203_GM18523_YRI	100.0%	100.0%	100.0%	39.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_212_GM18873_YRI	100.0%	100.0%	100.0%	44.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_216_GM18878_YRI	100.0%	100.0%	100.0%	70.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_220_GM18909_YRI	100.0%	100.0%	100.0%	39.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	30.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_228_GM18933_YRI	100.0%	100.0%	100.0%	37.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_236_GM19095_YRI	100.0%	100.0%	100.0%	46.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_239_GM19099_YRI	100.0%	100.0%	100.0%	51.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R2_240_GM19102_YRI	100.0%	100.0%	100.0%	41.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_93_HG03111_ESN	100.0%	100.0%	100.0%	40.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_115_HG03162_ESN	100.0%	100.0%	100.0%	33.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_166_HG03517_ESN	100.0%	100.0%	100.0%	39.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_194_GM18505_YRI	100.0%	100.0%	100.0%	39.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_197_GM18511_YRI	100.0%	100.0%	100.0%	45.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_199_GM18517_YRI	100.0%	100.0%	100.0%	43.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_201_GM18520_YRI	100.0%	100.0%	100.0%	32.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_203_GM18523_YRI	100.0%	100.0%	100.0%	50.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_212_GM18873_YRI	100.0%	100.0%	100.0%	39.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	100.0%	100.0%	100.0%	49.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_220_GM18909_YRI	100.0%	100.0%	100.0%	52.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	71.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_228_GM18933_YRI	100.0%	100.0%	100.0%	49.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_236_GM19095_YRI	100.0%	100.0%	100.0%	36.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_239_GM19099_YRI	100.0%	100.0%	100.0%	70.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
CTL_0_S2_P1_R3_240_GM19102_YRI	100.0%	100.0%	100.0%	38.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	100.0%	100.0%	100.0%	53.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	100.0%	100.0%	100.0%	29.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	100.0%	100.0%	100.0%	40.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	100.0%	100.0%	100.0%	41.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	100.0%	100.0%	100.0%	44.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	100.0%	100.0%	100.0%	50.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	100.0%	100.0%	100.0%	42.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	100.0%	100.0%	100.0%	30.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	100.0%	100.0%	100.0%	38.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	100.0%	100.0%	100.0%	65.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	100.0%	100.0%	100.0%	36.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	38.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	100.0%	100.0%	100.0%	35.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	100.0%	100.0%	100.0%	36.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	100.0%	100.0%	100.0%	35.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	100.0%	100.0%	100.0%	43.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	100.0%	100.0%	100.0%	37.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	100.0%	100.0%	100.0%	42.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	100.0%	100.0%	100.0%	39.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	100.0%	100.0%	100.0%	43.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	100.0%	100.0%	100.0%	50.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	100.0%	100.0%	100.0%	47.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	100.0%	100.0%	100.0%	34.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	100.0%	100.0%	100.0%	42.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	100.0%	100.0%	100.0%	37.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	100.0%	100.0%	100.0%	26.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	100.0%	100.0%	100.0%	31.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	40.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	100.0%	100.0%	100.0%	33.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	100.0%	100.0%	100.0%	47.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	100.0%	100.0%	100.0%	42.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	100.0%	100.0%	100.0%	48.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	100.0%	100.0%	100.0%	59.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	100.0%	100.0%	100.0%	49.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	100.0%	100.0%	100.0%	62.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	100.0%	100.0%	100.0%	57.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	100.0%	100.0%	100.0%	55.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	100.0%	100.0%	100.0%	42.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	100.0%	100.0%	100.0%	58.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	100.0%	100.0%	100.0%	65.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	100.0%	100.0%	100.0%	58.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	100.0%	100.0%	100.0%	68.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	100.0%	100.0%	100.0%	58.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	58.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	100.0%	100.0%	100.0%	49.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	100.0%	100.0%	100.0%	46.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	100.0%	100.0%	100.0%	50.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	100.0%	100.0%	100.0%	42.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	100.0%	100.0%	100.0%	63.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	100.0%	100.0%	100.0%	61.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	100.0%	100.0%	100.0%	61.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	100.0%	100.0%	100.0%	56.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	100.0%	100.0%	100.0%	61.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	100.0%	100.0%	100.0%	58.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	100.0%	100.0%	100.0%	64.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	100.0%	100.0%	100.0%	67.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	100.0%	100.0%	100.0%	58.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	100.0%	100.0%	100.0%	62.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	100.0%	100.0%	100.0%	61.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	61.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	100.0%	100.0%	100.0%	59.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	100.0%	100.0%	100.0%	58.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	100.0%	100.0%	100.0%	61.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	100.0%	100.0%	100.0%	45.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	100.0%	100.0%	100.0%	59.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	100.0%	100.0%	100.0%	41.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	100.0%	100.0%	100.0%	33.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	100.0%	100.0%	100.0%	37.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	100.0%	100.0%	100.0%	42.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	100.0%	100.0%	100.0%	57.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	100.0%	100.0%	100.0%	42.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	100.0%	100.0%	100.0%	29.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	100.0%	100.0%	100.0%	48.8%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	100.0%	100.0%	100.0%	65.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	100.0%	100.0%	100.0%	39.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	40.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	100.0%	100.0%	100.0%	39.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	100.0%	100.0%	100.0%	38.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	100.0%	100.0%	100.0%	38.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	100.0%	100.0%	100.0%	46.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	100.0%	100.0%	100.0%	43.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	100.0%	100.0%	100.0%	38.5%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	100.0%	100.0%	100.0%	38.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	100.0%	100.0%	100.0%	39.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	100.0%	100.0%	100.0%	40.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	100.0%	100.0%	100.0%	44.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	100.0%	100.0%	100.0%	48.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	100.0%	100.0%	100.0%	42.2%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	100.0%	100.0%	100.0%	48.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	100.0%	100.0%	100.0%	39.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	100.0%	100.0%	100.0%	41.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	100.0%	100.0%	100.0%	44.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	100.0%	100.0%	100.0%	48.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	100.0%	100.0%	100.0%	40.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	100.0%	100.0%	100.0%	30.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	100.0%	100.0%	100.0%	67.3%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-flagstat-pct-table_table

Sort	Column	Description	ID
\|\|	Total Reads	Total Reads	`flagstat_total_pct`
\|\|	Total Passed QC	Total Passed QC	`total_passed_pct`
\|\|	Mapped	Mapped	`mapped_passed_pct`
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed_pct`
\|\|	Duplicates	Duplicates	`duplicates_passed_pct`
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed_pct`
\|\|	Properly Paired	Properly Paired	`properly_paired_passed_pct`
\|\|	Self and mate mapped	Self and mate mapped	`with_itself_and_mate_mapped_passed_pct`
\|\|	Singletons	Singletons	`singletons_passed_pct`
\|\|	Mate mapped to diff chr	Mate mapped to diff chr	`with_mate_mapped_to_a_different_chr_passed_pct`
\|\|	Diff chr (mapQ >= 5)	Diff chr (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed_pct`

Mapped reads per contig

The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

Created with MultiQC

STAR

Universal RNA-seq aligner.https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

Summary Statistics

Summary statistics from the STAR alignment

Showing ¹²⁸/₁₂₈ rows and ¹⁰/₁₉ columns.

Sample Name	Total reads	Aligned	Aligned	Uniq aligned	Uniq aligned	Multimapped	Avg. read len	Avg. mapped len	Splices	Annotated splices	GT/AG splices	GC/AG splices	AT/AC splices	Non-canonical splices	Mismatch rate	Del rate	Del len	Ins rate	Ins len
CTL_0_S2_P1_R2_93_HG03111_ESN	4.4M	4.1M	93.6%	3.4M	78.5%	0.7M	104.0bp	112.0bp	0.8M	0.8M	0.8M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.9bp
CTL_0_S2_P1_R2_115_HG03162_ESN	6.1M	5.9M	95.7%	4.9M	80.8%	0.9M	106.0bp	110.9bp	1.4M	1.4M	1.4M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.9bp
CTL_0_S2_P1_R2_166_HG03517_ESN	4.0M	3.9M	95.8%	3.3M	81.2%	0.6M	111.0bp	116.0bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.1bp
CTL_0_S2_P1_R2_194_GM18505_YRI	6.7M	6.4M	95.8%	5.4M	81.3%	1.0M	105.0bp	110.8bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.9bp
CTL_0_S2_P1_R2_197_GM18511_YRI	3.0M	2.7M	90.7%	2.2M	74.8%	0.5M	103.0bp	113.6bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.9bp
CTL_0_S2_P1_R2_199_GM18517_YRI	3.5M	3.3M	92.8%	2.7M	77.5%	0.5M	105.0bp	113.0bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.2bp
CTL_0_S2_P1_R2_201_GM18520_YRI	2.9M	2.5M	86.3%	2.0M	70.0%	0.5M	96.0bp	112.5bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.3bp
CTL_0_S2_P1_R2_203_GM18523_YRI	3.8M	3.4M	91.1%	2.8M	75.8%	0.6M	99.0bp	108.8bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.9bp
CTL_0_S2_P1_R2_212_GM18873_YRI	4.8M	4.3M	90.8%	3.6M	75.5%	0.7M	97.0bp	107.3bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.5bp
CTL_0_S2_P1_R2_216_GM18878_YRI	1.1M	0.5M	45.2%	0.2M	18.1%	0.3M	28.0bp	39.2bp	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	1.0%	0.0%	1.2bp	0.0%	1.3bp
CTL_0_S2_P1_R2_220_GM18909_YRI	3.2M	3.0M	94.0%	2.6M	80.2%	0.4M	108.0bp	114.8bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.2bp
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	7.2M	7.0M	97.0%	6.0M	83.2%	1.0M	106.0bp	109.8bp	1.4M	1.4M	1.4M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	2.2bp
CTL_0_S2_P1_R2_228_GM18933_YRI	5.0M	4.7M	95.1%	4.0M	80.3%	0.7M	106.0bp	111.8bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.2bp
CTL_0_S2_P1_R2_236_GM19095_YRI	3.0M	2.7M	89.7%	2.2M	74.9%	0.4M	99.0bp	110.6bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.1%	2.0bp
CTL_0_S2_P1_R2_239_GM19099_YRI	3.3M	2.8M	83.6%	2.2M	67.0%	0.6M	89.0bp	107.7bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.6bp	0.0%	2.0bp
CTL_0_S2_P1_R2_240_GM19102_YRI	5.0M	4.6M	90.8%	3.8M	74.9%	0.8M	100.0bp	109.5bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.3bp
CTL_0_S2_P1_R3_93_HG03111_ESN	3.4M	3.2M	94.4%	2.8M	82.2%	0.4M	110.0bp	115.8bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.0%	2.0bp
CTL_0_S2_P1_R3_115_HG03162_ESN	6.5M	6.3M	97.0%	5.4M	82.5%	0.9M	110.0bp	114.0bp	1.6M	1.6M	1.6M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.1%	1.9bp
CTL_0_S2_P1_R3_166_HG03517_ESN	4.5M	4.4M	96.1%	3.8M	82.6%	0.6M	113.0bp	117.5bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	1.1bp
CTL_0_S2_P1_R3_194_GM18505_YRI	6.3M	6.0M	95.7%	5.2M	82.6%	0.8M	111.0bp	115.9bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.9bp
CTL_0_S2_P1_R3_197_GM18511_YRI	4.0M	3.7M	92.8%	3.1M	78.2%	0.6M	108.0bp	115.8bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.9bp
CTL_0_S2_P1_R3_199_GM18517_YRI	3.2M	3.0M	93.5%	2.5M	78.0%	0.5M	109.0bp	116.5bp	0.8M	0.8M	0.8M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.0%	1.1bp
CTL_0_S2_P1_R3_201_GM18520_YRI	8.2M	8.0M	97.3%	6.6M	80.3%	1.4M	109.0bp	113.6bp	1.9M	1.9M	1.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.2bp
CTL_0_S2_P1_R3_203_GM18523_YRI	3.1M	2.5M	80.7%	2.0M	64.5%	0.5M	83.0bp	103.3bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.0%	1.8bp
CTL_0_S2_P1_R3_212_GM18873_YRI	5.2M	4.9M	94.6%	4.2M	80.4%	0.7M	108.0bp	114.6bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	2.6bp
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	5.3M	4.8M	89.5%	3.9M	73.3%	0.9M	101.0bp	113.7bp	1.4M	1.4M	1.4M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.1%	2.6bp
CTL_0_S2_P1_R3_220_GM18909_YRI	5.1M	4.5M	87.4%	3.7M	71.5%	0.8M	99.0bp	113.0bp	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	2.3bp
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	1.4M	0.5M	35.1%	0.2M	11.6%	0.3M	25.0bp	18.6bp	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	2.0%	0.0%	1.0bp	0.0%	1.0bp
CTL_0_S2_P1_R3_228_GM18933_YRI	4.8M	4.3M	89.5%	3.6M	74.4%	0.7M	102.0bp	114.7bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.1bp
CTL_0_S2_P1_R3_236_GM19095_YRI	6.3M	6.0M	95.5%	5.1M	82.0%	0.8M	109.0bp	114.5bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.1%	2.0bp
CTL_0_S2_P1_R3_239_GM19099_YRI	1.4M	0.6M	40.5%	0.2M	13.0%	0.4M	25.0bp	18.8bp	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	1.9%	0.0%	1.0bp	0.0%	1.0bp
CTL_0_S2_P1_R3_240_GM19102_YRI	5.4M	5.1M	93.0%	4.3M	78.8%	0.8M	103.0bp	110.9bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.3bp
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	3.6M	3.0M	84.1%	2.4M	67.5%	0.6M	92.0bp	110.2bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.8bp
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	7.1M	6.9M	96.7%	5.9M	83.3%	0.9M	106.0bp	109.7bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	1.8bp
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	4.4M	4.2M	93.7%	3.5M	79.1%	0.6M	105.0bp	112.5bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	2.1bp	0.0%	1.2bp
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	3.6M	3.4M	92.9%	2.9M	79.0%	0.5M	103.0bp	111.7bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	2.2bp
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	5.4M	5.0M	92.3%	4.2M	78.6%	0.7M	104.0bp	112.4bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.8bp
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	3.2M	2.8M	86.6%	2.3M	70.2%	0.5M	93.0bp	108.8bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.3bp
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	3.2M	3.0M	91.7%	2.5M	77.1%	0.5M	100.0bp	110.0bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.4%	0.0%	2.0bp	0.0%	1.4bp
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	6.8M	6.5M	95.9%	5.5M	80.6%	1.0M	104.0bp	109.5bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.8bp
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	5.1M	4.8M	93.5%	4.1M	79.3%	0.7M	106.0bp	113.4bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	2.0bp	0.0%	2.3bp
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	2.7M	1.6M	60.4%	1.1M	41.9%	0.5M	60.0bp	96.9bp	0.3M	0.3M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.4bp
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	4.9M	4.6M	95.0%	4.0M	82.4%	0.6M	109.0bp	114.7bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.1bp
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	6.4M	6.0M	94.7%	5.2M	82.0%	0.8M	107.0bp	112.8bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	2.1bp
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	5.4M	5.2M	95.2%	4.4M	82.0%	0.7M	107.0bp	112.8bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.4%	0.0%	2.0bp	0.0%	1.2bp
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	4.2M	3.9M	93.9%	3.4M	81.0%	0.5M	105.0bp	112.3bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.4%	0.0%	2.0bp	0.0%	1.9bp
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	4.5M	4.3M	94.4%	3.7M	81.2%	0.6M	106.0bp	112.7bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.9bp
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	3.5M	3.1M	88.7%	2.6M	73.1%	0.5M	99.0bp	112.0bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.3bp
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	4.6M	4.4M	96.5%	3.8M	82.6%	0.6M	112.0bp	117.0bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.9bp
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	4.0M	3.8M	94.0%	3.2M	79.0%	0.6M	111.0bp	118.3bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	2.1bp	0.0%	1.9bp
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	4.7M	4.5M	95.8%	3.9M	82.2%	0.6M	112.0bp	116.8bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	2.1bp	0.0%	1.2bp
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	5.5M	5.1M	93.9%	4.4M	79.7%	0.8M	108.0bp	115.2bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.4%	0.0%	2.0bp	0.0%	2.4bp
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	3.2M	2.9M	89.9%	2.4M	75.3%	0.5M	102.0bp	113.3bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	1.9bp
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	5.4M	5.0M	92.0%	4.2M	76.7%	0.8M	104.0bp	113.4bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.1bp
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	6.0M	5.8M	96.5%	4.9M	82.3%	0.9M	110.0bp	114.0bp	1.4M	1.4M	1.4M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.6bp
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	4.2M	3.8M	91.2%	3.2M	77.2%	0.6M	103.0bp	112.5bp	0.8M	0.8M	0.8M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.8bp
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	7.2M	6.9M	96.3%	5.9M	82.2%	1.0M	114.0bp	118.3bp	2.3M	2.3M	2.3M	0.0M	0.0M	0.0M	0.3%	0.0%	2.0bp	0.0%	2.3bp
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	7.7M	7.5M	97.6%	6.7M	86.5%	0.9M	113.0bp	115.6bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	2.5bp
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	6.8M	6.6M	97.4%	5.8M	84.7%	0.9M	116.0bp	118.6bp	1.8M	1.8M	1.8M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.2bp
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	6.1M	5.7M	94.4%	5.0M	81.8%	0.8M	110.0bp	116.3bp	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.1bp
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	8.6M	8.3M	96.8%	7.2M	83.8%	1.1M	113.0bp	117.1bp	2.0M	2.0M	2.0M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	1.2bp
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	3.4M	3.1M	91.8%	2.6M	77.3%	0.5M	107.0bp	116.8bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	2.0bp	0.0%	1.9bp
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	4.5M	4.2M	93.2%	3.6M	78.8%	0.7M	109.0bp	117.4bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.9bp
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	4.0M	3.5M	86.1%	2.8M	69.5%	0.7M	99.0bp	115.2bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.3bp
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	2.6M	1.9M	73.0%	1.4M	54.1%	0.5M	67.0bp	94.7bp	0.2M	0.2M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.6bp	0.0%	1.8bp
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	4.7M	4.1M	86.6%	3.3M	69.4%	0.8M	84.0bp	98.4bp	0.6M	0.6M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	2.7M	2.0M	74.1%	1.5M	55.0%	0.5M	69.0bp	94.1bp	0.2M	0.2M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.1bp
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	3.2M	2.6M	81.0%	2.1M	64.4%	0.5M	81.0bp	101.0bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	3.6M	3.0M	81.7%	2.4M	66.3%	0.6M	82.0bp	101.2bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	2.0bp	0.0%	1.8bp
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	3.9M	3.5M	90.4%	2.9M	75.5%	0.6M	96.0bp	106.7bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.1bp
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	2.5M	1.9M	78.3%	1.5M	60.5%	0.4M	78.0bp	101.1bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.5bp
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	2.2M	1.3M	60.1%	0.9M	40.3%	0.4M	54.0bp	90.8bp	0.1M	0.1M	0.1M	0.0M	0.0M	0.0M	0.5%	0.0%	1.3bp	0.0%	1.6bp
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	2.6M	1.9M	74.5%	1.5M	59.1%	0.4M	77.0bp	102.3bp	0.2M	0.2M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.5bp	0.0%	2.4bp
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	1.6M	0.8M	52.7%	0.5M	33.7%	0.3M	49.0bp	92.7bp	0.1M	0.1M	0.1M	0.0M	0.0M	0.0M	0.4%	0.0%	1.2bp	0.0%	1.0bp
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	3.8M	3.1M	81.0%	2.5M	64.3%	0.6M	82.0bp	101.9bp	0.4M	0.4M	0.4M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	2.2bp
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	3.3M	2.6M	77.8%	2.0M	61.7%	0.5M	79.0bp	100.8bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	2.2bp
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	3.1M	2.7M	86.9%	2.2M	71.8%	0.5M	91.0bp	104.4bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.1bp
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	4.7M	4.2M	89.4%	3.5M	75.8%	0.6M	95.0bp	106.2bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	3.7M	3.0M	82.0%	2.5M	67.4%	0.5M	86.0bp	103.2bp	0.4M	0.4M	0.4M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	3.6M	3.2M	88.7%	2.6M	73.6%	0.5M	95.0bp	106.6bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.2bp
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	2.9M	2.1M	72.7%	1.5M	52.3%	0.6M	70.0bp	98.8bp	0.4M	0.4M	0.4M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	3.4M	2.6M	73.9%	1.9M	54.5%	0.7M	70.0bp	96.1bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	2.7M	2.0M	74.9%	1.6M	57.9%	0.5M	77.0bp	101.6bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	2.3bp	0.0%	1.1bp
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	3.7M	3.1M	84.4%	2.5M	68.5%	0.6M	89.0bp	105.5bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	3.6M	2.8M	76.5%	2.1M	57.7%	0.7M	74.0bp	98.1bp	0.4M	0.4M	0.4M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	2.5M	2.0M	79.4%	1.5M	62.0%	0.4M	82.0bp	103.0bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.6%	0.0%	2.3bp	0.0%	1.1bp
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	2.1M	1.3M	61.9%	0.9M	42.3%	0.4M	60.0bp	93.2bp	0.2M	0.2M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.2bp
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	2.3M	1.4M	60.9%	0.9M	39.3%	0.5M	52.0bp	84.1bp	0.1M	0.1M	0.1M	0.0M	0.0M	0.0M	0.6%	0.0%	1.5bp	0.0%	1.6bp
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	3.0M	2.3M	77.7%	1.9M	62.3%	0.5M	81.0bp	103.7bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.6bp	0.0%	2.5bp
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	2.3M	1.7M	73.5%	1.3M	55.3%	0.4M	75.0bp	102.4bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.6bp	0.0%	2.5bp
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	2.1M	1.6M	76.8%	1.3M	59.7%	0.4M	80.0bp	104.4bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.1bp
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	3.1M	2.3M	75.5%	1.8M	59.0%	0.5M	80.0bp	105.2bp	0.4M	0.4M	0.4M	0.0M	0.0M	0.0M	0.4%	0.0%	2.1bp	0.0%	2.1bp
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	2.7M	2.1M	78.9%	1.7M	61.8%	0.5M	84.0bp	105.6bp	0.4M	0.4M	0.4M	0.0M	0.0M	0.0M	0.5%	0.0%	2.0bp	0.0%	1.2bp
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	3.6M	2.9M	79.7%	2.3M	63.5%	0.6M	83.0bp	105.0bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	2.3M	1.7M	71.4%	1.3M	54.4%	0.4M	76.0bp	105.6bp	0.3M	0.3M	0.3M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	4.4M	3.9M	89.2%	3.3M	74.4%	0.7M	98.0bp	109.9bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.2bp
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	2.2M	1.7M	76.7%	1.3M	59.2%	0.4M	79.0bp	103.2bp	0.2M	0.2M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	5.4M	5.0M	92.2%	4.2M	77.4%	0.8M	103.0bp	111.8bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	5.2M	5.0M	96.5%	4.1M	80.2%	0.8M	104.0bp	109.7bp	1.0M	1.0M	0.9M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.1bp
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	4.1M	3.9M	93.9%	3.4M	81.0%	0.5M	106.0bp	113.5bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	2.0bp
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	4.4M	4.1M	93.3%	3.5M	78.1%	0.7M	105.0bp	112.0bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	1.9bp
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	2.8M	2.2M	77.9%	1.7M	61.1%	0.5M	82.0bp	107.1bp	0.4M	0.4M	0.4M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.0%	1.1bp
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	4.0M	3.7M	92.1%	3.0M	76.4%	0.6M	100.0bp	109.5bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	1.3bp
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	5.0M	4.8M	96.5%	4.1M	80.8%	0.8M	104.0bp	109.5bp	0.8M	0.8M	0.7M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.9bp
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	4.2M	3.5M	83.8%	2.9M	68.0%	0.7M	86.0bp	104.0bp	0.6M	0.6M	0.6M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.6bp
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	2.0M	1.3M	65.6%	0.9M	44.2%	0.4M	59.0bp	89.3bp	0.2M	0.2M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.2bp
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	6.2M	5.8M	93.3%	4.9M	78.7%	0.9M	102.0bp	110.5bp	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.2bp
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	6.5M	6.1M	93.6%	5.2M	79.6%	0.9M	101.0bp	109.0bp	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	2.2bp
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	4.5M	4.2M	93.4%	3.6M	78.7%	0.7M	101.0bp	108.6bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.2bp
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	4.8M	4.5M	93.3%	3.9M	80.3%	0.6M	103.0bp	110.7bp	0.8M	0.8M	0.8M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.1%	2.0bp
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	4.2M	3.9M	93.3%	3.3M	79.2%	0.6M	100.0bp	107.6bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.1%	2.0bp
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	4.3M	3.7M	86.8%	3.1M	71.2%	0.7M	96.0bp	110.0bp	0.7M	0.7M	0.7M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.2bp
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	3.4M	3.2M	94.1%	2.7M	78.7%	0.5M	111.0bp	118.5bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.0bp
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	5.1M	4.9M	95.3%	4.1M	81.1%	0.7M	109.0bp	114.7bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.1%	2.0bp
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	5.6M	5.4M	96.2%	4.5M	80.2%	0.9M	114.0bp	119.1bp	1.6M	1.6M	1.6M	0.0M	0.0M	0.0M	0.4%	0.0%	2.1bp	0.0%	1.6bp
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	4.0M	3.8M	95.9%	3.3M	82.7%	0.5M	112.0bp	117.1bp	0.9M	0.9M	0.9M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.0%	2.0bp
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	3.8M	3.6M	95.3%	3.0M	80.4%	0.6M	113.0bp	118.8bp	1.2M	1.2M	1.2M	0.0M	0.0M	0.0M	0.4%	0.0%	1.6bp	0.0%	1.9bp
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	3.9M	3.6M	92.8%	3.1M	77.9%	0.6M	109.0bp	117.3bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.5%	0.0%	1.9bp	0.0%	1.1bp
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	3.9M	3.5M	88.8%	2.8M	71.9%	0.7M	99.0bp	112.4bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.0%	1.3bp
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	3.0M	2.8M	92.4%	2.3M	77.3%	0.5M	103.0bp	111.8bp	0.5M	0.5M	0.5M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.0%	1.9bp
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	4.5M	4.0M	89.3%	3.3M	74.1%	0.7M	99.0bp	111.7bp	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.1%	2.6bp
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	5.6M	5.3M	94.8%	4.5M	81.5%	0.7M	108.0bp	113.9bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.1%	2.7bp
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	5.5M	5.2M	94.6%	4.4M	80.3%	0.8M	111.0bp	117.2bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.9bp	0.1%	2.3bp
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	5.0M	4.6M	92.6%	3.9M	78.3%	0.7M	107.0bp	115.2bp	1.3M	1.3M	1.3M	0.0M	0.0M	0.0M	0.4%	0.0%	1.8bp	0.1%	2.2bp
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	4.3M	3.8M	89.7%	3.2M	74.1%	0.7M	102.0bp	114.9bp	1.0M	1.0M	1.0M	0.0M	0.0M	0.0M	0.5%	0.0%	1.8bp	0.0%	1.1bp
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	5.2M	4.9M	93.9%	4.2M	80.9%	0.7M	109.0bp	115.8bp	1.1M	1.1M	1.1M	0.0M	0.0M	0.0M	0.5%	0.0%	2.0bp	0.1%	2.0bp
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	8.4M	8.2M	97.3%	7.1M	84.1%	1.1M	110.0bp	113.1bp	1.8M	1.8M	1.8M	0.0M	0.0M	0.0M	0.4%	0.0%	1.7bp	0.1%	2.0bp
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	2.2M	1.2M	54.2%	0.7M	32.2%	0.5M	53.0bp	91.4bp	0.2M	0.2M	0.2M	0.0M	0.0M	0.0M	0.5%	0.0%	1.7bp	0.0%	1.2bp

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: star_summary_table_table

Sort	Column	Description	ID	Scale
\|\|	Total reads	Number of input reads	`star-total_reads`	read_count
\|\|	Aligned	Mapped reads	`star-mapped`	read_count
\|\|	Aligned	% Mapped reads	`star-mapped_percent`
\|\|	Uniq aligned	Uniquely mapped reads	`star-uniquely_mapped`	read_count
\|\|	Uniq aligned	% Uniquely mapped reads	`star-uniquely_mapped_percent`
\|\|	Multimapped	Multiple mapped reads	`star-multimapped`	read_count
\|\|	Avg. read len	Average input read length	`star-avg_input_read_length`
\|\|	Avg. mapped len	Average mapped length	`star-avg_mapped_read_length`
\|\|	Splices	Number of splices: Total	`star-num_splices`	read_count
\|\|	Annotated splices	Number of splices: Annotated (sjdb)	`star-num_annotated_splices`	read_count
\|\|	GT/AG splices	Number of splices: GT/AG	`star-num_GTAG_splices`	read_count
\|\|	GC/AG splices	Number of splices: GC/AG	`star-num_GCAG_splices`	read_count
\|\|	AT/AC splices	Number of splices: AT/AC	`star-num_ATAC_splices`	read_count
\|\|	Non-canonical splices	Number of splices: Non-canonical	`star-num_noncanonical_splices`	read_count
\|\|	Mismatch rate	Mismatch rate per base	`star-mismatch_rate`
\|\|	Del rate	Deletion rate per base	`star-deletion_rate`
\|\|	Del len	Deletion average length	`star-deletion_length`
\|\|	Ins rate	Insertion rate per base	`star-insertion_rate`
\|\|	Ins len	Insertion average length	`star-insertion_length`

Alignment Scores

Created with MultiQC

UMI-tools

Tools for dealing with Unique Molecular Identifiers (UMIs)/(RMTs) and scRNA-Seq barcodes.https://github.com/CGATOxford/UMI-toolsDOI: 10.1101/gr.209601.116

Deduplicated Reads

Created with MultiQC

UMI Stats

Statistics from running umi_tools dedup or umi_tools extract

Positions Dedup: Total number of positions deduplicated
Total UMIs: Total UMIs found in sample
Unique UMIs: Unique UMIs found in sample
Mean #UMI: Mean number of unique UMIs per position
Max #UMI: Max number of unique UMIs per position

Created with MultiQC

Showing ¹²⁸/₁₂₈ rows and ⁵/₅ columns.

Sample Name	Positions Dedup	Total UMIs	Unique UMIs	Mean #UMI	Max #UMI
CTL_0_S2_P1_R2_93_HG03111_ESN	754852	5752666	5400	1.58	953
CTL_0_S2_P1_R2_115_HG03162_ESN	1439014	8167762	5718	1.99	2347
CTL_0_S2_P1_R2_166_HG03517_ESN	471113	5283894	5380	1.70	855
CTL_0_S2_P1_R2_194_GM18505_YRI	1068371	8906617	5820	1.77	1572
CTL_0_S2_P1_R2_197_GM18511_YRI	355699	3956424	5152	1.53	1204
CTL_0_S2_P1_R2_199_GM18517_YRI	504012	4617355	5278	1.65	820
CTL_0_S2_P1_R2_201_GM18520_YRI	359745	3808180	5040	1.51	1116
CTL_0_S2_P1_R2_203_GM18523_YRI	791568	4881445	5319	1.74	1588
CTL_0_S2_P1_R2_212_GM18873_YRI	658013	6420718	5502	1.65	1283
CTL_0_S2_P1_R2_216_GM18878_YRI	302633	1431381	4335	1.54	1781
CTL_0_S2_P1_R2_220_GM18909_YRI	412888	4151103	5170	1.56	767
CTL_0_S2_P1_R2_220_GM18909_YRI_extra	1234364	9371833	5901	1.88	2237
CTL_0_S2_P1_R2_228_GM18933_YRI	707604	6525851	5576	1.67	948
CTL_0_S2_P1_R2_236_GM19095_YRI	430018	3823277	5138	1.46	1251
CTL_0_S2_P1_R2_239_GM19099_YRI	512382	4306456	5149	1.51	1510
CTL_0_S2_P1_R2_240_GM19102_YRI	798092	6674424	5569	1.66	1442
CTL_0_S2_P1_R3_93_HG03111_ESN	245530	4182209	5226	1.44	638
CTL_0_S2_P1_R3_115_HG03162_ESN	983750	8605064	5783	2.10	1589
CTL_0_S2_P1_R3_166_HG03517_ESN	453949	5887589	5466	1.74	696
CTL_0_S2_P1_R3_194_GM18505_YRI	621481	8126693	5759	1.68	736
CTL_0_S2_P1_R3_197_GM18511_YRI	424010	5232622	5375	1.61	1187
CTL_0_S2_P1_R3_199_GM18517_YRI	246720	4237614	5180	1.57	485
CTL_0_S2_P1_R3_201_GM18520_YRI	1275073	11091005	5963	2.08	2162
CTL_0_S2_P1_R3_203_GM18523_YRI	501958	3932795	5061	1.61	1233
CTL_0_S2_P1_R3_212_GM18873_YRI	568287	6811752	5577	1.58	893
CTL_0_S2_P1_R3_212_GM18873_YRI_extra	544711	7047539	5491	1.67	662
CTL_0_S2_P1_R3_220_GM18909_YRI	486663	6684315	5499	1.56	1288
CTL_0_S2_P1_R3_220_GM18909_YRI_extra	402142	1673377	4374	1.55	1464
CTL_0_S2_P1_R3_228_GM18933_YRI	459228	6181299	5520	1.51	1083
CTL_0_S2_P1_R3_236_GM19095_YRI	748394	8041289	5741	1.66	998
CTL_0_S2_P1_R3_239_GM19099_YRI	396784	1886556	4389	1.49	1638
CTL_0_S2_P1_R3_240_GM19102_YRI	927948	7072059	5582	1.57	1565
PTX006_0-004_S2_P1_R2_93_HG03111_ESN	493625	4616506	5161	1.56	1597
PTX006_0-004_S2_P1_R2_115_HG03162_ESN	1506747	9228131	5846	1.78	2445
PTX006_0-004_S2_P1_R2_166_HG03517_ESN	583469	5783812	5487	1.64	1012
PTX006_0-004_S2_P1_R2_194_GM18505_YRI	610881	4647743	5301	1.48	975
PTX006_0-004_S2_P1_R2_197_GM18511_YRI	558129	6889881	5603	1.59	1093
PTX006_0-004_S2_P1_R2_199_GM18517_YRI	492815	4240397	5188	1.48	780
PTX006_0-004_S2_P1_R2_201_GM18520_YRI	503776	4192145	5162	1.50	590
PTX006_0-004_S2_P1_R2_203_GM18523_YRI	1489808	8856460	5838	1.80	2951
PTX006_0-004_S2_P1_R2_212_GM18873_YRI	668203	6653811	5562	1.75	978
PTX006_0-004_S2_P1_R2_216_GM18878_YRI	341507	3047056	4791	1.51	1795
PTX006_0-004_S2_P1_R2_220_GM18909_YRI	428048	6088973	5555	1.56	786
PTX006_0-004_S2_P1_R2_220_GM18909_YRI_extra	686379	8040294	5759	1.59	727
PTX006_0-004_S2_P1_R2_228_GM18933_YRI	689334	6865759	5633	1.57	1006
PTX006_0-004_S2_P1_R2_236_GM19095_YRI	592258	5244693	5398	1.51	764
PTX006_0-004_S2_P1_R2_239_GM19099_YRI	630349	5733430	5488	1.62	1196
PTX006_0-004_S2_P1_R2_240_GM19102_YRI	571771	4511177	5293	1.59	974
PTX006_0-004_S2_P1_R3_93_HG03111_ESN	385197	6000472	5533	1.75	677
PTX006_0-004_S2_P1_R3_115_HG03162_ESN	425868	5281124	5337	1.76	1055
PTX006_0-004_S2_P1_R3_166_HG03517_ESN	379037	6090712	5437	1.63	531
PTX006_0-004_S2_P1_R3_194_GM18505_YRI	499651	7129886	5645	1.63	461
PTX006_0-004_S2_P1_R3_197_GM18511_YRI	342248	4173237	5178	1.44	1113
PTX006_0-004_S2_P1_R3_199_GM18517_YRI	522126	7142227	5644	1.66	1370
PTX006_0-004_S2_P1_R3_201_GM18520_YRI	846805	7821889	5710	1.82	1434
PTX006_0-004_S2_P1_R3_203_GM18523_YRI	534680	5288485	5342	1.71	1269
PTX006_0-004_S2_P1_R3_212_GM18873_YRI	562532	9352911	5810	1.87	867
PTX006_0-004_S2_P1_R3_212_GM18873_YRI_extra	991824	9515222	5935	1.61	1297
PTX006_0-004_S2_P1_R3_220_GM18909_YRI	647447	8641093	5824	1.79	647
PTX006_0-004_S2_P1_R3_220_GM18909_YRI_extra	541514	7598248	5705	1.44	1127
PTX006_0-004_S2_P1_R3_228_GM18933_YRI	936885	10934964	6055	1.72	943
PTX006_0-004_S2_P1_R3_236_GM19095_YRI	293165	4335825	5199	1.43	1157
PTX006_0-004_S2_P1_R3_239_GM19099_YRI	436367	5844227	5427	1.64	968
PTX006_0-004_S2_P1_R3_240_GM19102_YRI	515109	5217206	5316	1.67	1935
PTX015_31-9_S2_P1_R2_93_HG03111_ESN	394580	3451614	4877	1.59	1694
PTX015_31-9_S2_P1_R2_115_HG03162_ESN	751780	6535150	5497	1.64	1556
PTX015_31-9_S2_P1_R2_166_HG03517_ESN	420148	3485527	4935	1.57	957
PTX015_31-9_S2_P1_R2_194_GM18505_YRI	448158	4140181	5142	1.47	864
PTX015_31-9_S2_P1_R2_197_GM18511_YRI	471367	4589714	5244	1.55	1051
PTX015_31-9_S2_P1_R2_199_GM18517_YRI	702227	4997381	5320	1.58	1460
PTX015_31-9_S2_P1_R2_201_GM18520_YRI	398412	3217635	4896	1.46	1232
PTX015_31-9_S2_P1_R2_203_GM18523_YRI	412400	2728324	4699	1.75	2019
PTX015_31-9_S2_P1_R2_212_GM18873_YRI	335327	3142167	4931	1.45	624
PTX015_31-9_S2_P1_R2_216_GM18878_YRI	266734	1840523	4493	1.61	1083
PTX015_31-9_S2_P1_R2_220_GM18909_YRI	405688	4890278	5268	1.40	1324
PTX015_31-9_S2_P1_R2_220_GM18909_YRI_extra	421541	4050004	5091	1.42	1149
PTX015_31-9_S2_P1_R2_228_GM18933_YRI	408695	3892488	5102	1.43	799
PTX015_31-9_S2_P1_R2_236_GM19095_YRI	503188	5829210	5483	1.47	1132
PTX015_31-9_S2_P1_R2_239_GM19099_YRI	497818	4530890	5213	1.51	1128
PTX015_31-9_S2_P1_R2_240_GM19102_YRI	593137	4539249	5280	1.53	965
PTX015_31-9_S2_P1_R3_93_HG03111_ESN	401830	3962896	5007	1.48	1270
PTX015_31-9_S2_P1_R3_115_HG03162_ESN	505456	4677930	5109	1.55	1619
PTX015_31-9_S2_P1_R3_166_HG03517_ESN	345120	3429669	4917	1.50	1240
PTX015_31-9_S2_P1_R3_194_GM18505_YRI	401359	4826491	5246	1.46	674
PTX015_31-9_S2_P1_R3_197_GM18511_YRI	545933	4926407	5164	1.55	1372
PTX015_31-9_S2_P1_R3_199_GM18517_YRI	345695	3156216	4905	1.45	1205
PTX015_31-9_S2_P1_R3_201_GM18520_YRI	335776	2548877	4711	1.53	856
PTX015_31-9_S2_P1_R3_203_GM18523_YRI	391742	2963310	4732	1.68	1356
PTX015_31-9_S2_P1_R3_212_GM18873_YRI	324312	3651021	5053	1.54	1110
PTX015_31-9_S2_P1_R3_212_GM18873_YRI_extra	371567	2869184	4870	1.41	1083
PTX015_31-9_S2_P1_R3_220_GM18909_YRI	282395	2683429	4779	1.40	1233
PTX015_31-9_S2_P1_R3_220_GM18909_YRI_extra	352332	3770401	5037	1.41	1082
PTX015_31-9_S2_P1_R3_228_GM18933_YRI	374076	3471108	4919	1.39	1232
PTX015_31-9_S2_P1_R3_236_GM19095_YRI	418249	4539677	5189	1.44	1064
PTX015_31-9_S2_P1_R3_239_GM19099_YRI	352394	2863402	4812	1.38	971
PTX015_31-9_S2_P1_R3_240_GM19102_YRI	549149	5569345	5411	1.52	1065
PXT001_0-04_S2_P1_R2_93_HG03111_ESN	384220	2876779	4832	1.40	1161
PXT001_0-04_S2_P1_R2_115_HG03162_ESN	770617	6994762	5606	1.69	1415
PXT001_0-04_S2_P1_R2_166_HG03517_ESN	927795	6899586	5602	1.85	2117
PXT001_0-04_S2_P1_R2_194_GM18505_YRI	630487	5232416	5381	1.62	686
PXT001_0-04_S2_P1_R2_197_GM18511_YRI	560387	5867543	5444	1.66	1105
PXT001_0-04_S2_P1_R2_199_GM18517_YRI	446875	3508301	4945	1.50	1058
PXT001_0-04_S2_P1_R2_201_GM18520_YRI	635095	5250517	5320	1.62	1016
PXT001_0-04_S2_P1_R2_203_GM18523_YRI	1136925	6545380	5610	1.85	2463
PXT001_0-04_S2_P1_R2_212_GM18873_YRI	645923	5453160	5383	1.47	1061
PXT001_0-04_S2_P1_R2_216_GM18878_YRI	391403	2710534	4704	1.59	1526
PXT001_0-04_S2_P1_R2_220_GM18909_YRI	668431	8026310	5725	1.57	1081
PXT001_0-04_S2_P1_R2_220_GM18909_YRI_extra	792027	8477333	5770	1.60	1213
PXT001_0-04_S2_P1_R2_228_GM18933_YRI	680457	5883659	5474	1.55	1431
PXT001_0-04_S2_P1_R2_236_GM19095_YRI	683297	6055024	5556	1.58	1156
PXT001_0-04_S2_P1_R2_239_GM19099_YRI	749392	5422079	5408	1.60	1069
PXT001_0-04_S2_P1_R2_240_GM19102_YRI	628384	5478887	5366	1.57	1133
PXT001_0-04_S2_P1_R3_93_HG03111_ESN	252965	4464098	5275	1.65	625
PXT001_0-04_S2_P1_R3_115_HG03162_ESN	604978	6641868	5540	1.79	1087
PXT001_0-04_S2_P1_R3_166_HG03517_ESN	413347	7341461	5679	1.87	587
PXT001_0-04_S2_P1_R3_194_GM18505_YRI	338999	5065920	5397	1.56	424
PXT001_0-04_S2_P1_R3_197_GM18511_YRI	313761	4940414	5348	1.73	406
PXT001_0-04_S2_P1_R3_199_GM18517_YRI	394255	5050840	5322	1.66	888
PXT001_0-04_S2_P1_R3_201_GM18520_YRI	596803	5226766	5294	1.70	1712
PXT001_0-04_S2_P1_R3_203_GM18523_YRI	364159	3916327	5166	1.60	668
PXT001_0-04_S2_P1_R3_212_GM18873_YRI	514352	5866873	5381	1.59	858
PXT001_0-04_S2_P1_R3_212_GM18873_YRI_extra	583038	7115537	5676	1.67	749
PXT001_0-04_S2_P1_R3_220_GM18909_YRI	427439	7087643	5635	1.60	657
PXT001_0-04_S2_P1_R3_220_GM18909_YRI_extra	442589	6444751	5495	1.56	772
PXT001_0-04_S2_P1_R3_228_GM18933_YRI	474683	5493237	5410	1.56	1241
PXT001_0-04_S2_P1_R3_236_GM19095_YRI	425699	6486531	5606	1.56	879
PXT001_0-04_S2_P1_R3_239_GM19099_YRI	1424235	10775973	6025	1.90	2309
PXT001_0-04_S2_P1_R3_240_GM19102_YRI	531896	2730923	4677	1.52	1788

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: umitools_stats_violin_table

Sort	Column	Description	ID
\|\|	Positions Dedup	Total number of positions deduplicated	`positions_deduplicated`
\|\|	Total UMIs	Total UMIs found in sample	`total_umis`
\|\|	Unique UMIs	Unique UMIs found in sample	`unique_umis`
\|\|	Mean #UMI	Mean number of unique UMIs per position	`mean_umi_per_pos`
\|\|	Max #UMI	Max number of unique UMIs per position	`max_umi_per_pos`

Sample relationships

Plots interrogating sample relationships, based on final count matrices.

STAR_SALMON DESeq2 sample similarity

is generated from clustering by Euclidean distances between DESeq2 rlog values for each sample in the deseq2_qc.r script.

Created with MultiQC

STAR_SALMON DESeq2 PCA plot

PCA plot between samples in the experiment. These values are calculated using DESeq2 in the deseq2_qc.r script.

Created with MultiQC

SortMeRNA

Program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data.http://bioinfo.lifl.fr/RNA/sortmernaDOI: 10.1093/bioinformatics/bts611

The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering ribosomal RNA from metatranscriptomic data.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Group	Software	Version
CUSTOM_GETCHROMSIZES	getchromsizes	`1.21`
CUSTOM_TX2GENE	python	`3.10.4`
DESEQ2_QC_STAR_SALMON	bioconductor-deseq2	`1.46.0`
	r-base	`4.4.2`
FASTQC_RAW	fastqc	`0.12.1`
FASTQC_TRIM	fastqc	`0.12.1`
FQ_LINT	fq	`0.12.0 (2024-07-08)`
FQ_SUBSAMPLE	fq	`0.12.0 (2024-07-08)`
GTF2BED	perl	`5.26.2`
GTF_FILTER	python	`3.9.5`
MAKE_TRANSCRIPTS_FASTA	rsem	`1.3.1`
	star	`2.7.10a`
PRESEQ_LCEXTRAP	preseq	`3.2.0`
QUALIMAP_RNASEQ	qualimap	`2.3`
RSEQC_BAMSTAT	rseqc	`5.0.2`
RSEQC_INFEREXPERIMENT	rseqc	`5.0.2`
RSEQC_INNERDISTANCE	rseqc	`5.0.2`
RSEQC_JUNCTIONANNOTATION	rseqc	`5.0.2`
RSEQC_JUNCTIONSATURATION	rseqc	`5.0.2`
RSEQC_READDISTRIBUTION	rseqc	`5.0.2`
RSEQC_READDUPLICATION	rseqc	`5.0.2`
SALMON_INDEX	salmon	`1.10.3`
SALMON_QUANT	salmon	`1.10.3`
SAMTOOLS_FLAGSTAT	samtools	`1.21`
SAMTOOLS_IDXSTATS	samtools	`1.21`
SAMTOOLS_INDEX	samtools	`1.21`
SAMTOOLS_SORT	samtools	`1.21`
SAMTOOLS_SORT_QUALIMAP	samtools	`1.21`
SAMTOOLS_STATS	samtools	`1.21`
SE_GENE_UNIFIED	bioconductor-summarizedexperiment	`1.32.0`
SE_TRANSCRIPT_UNIFIED	bioconductor-summarizedexperiment	`1.32.0`
SORTMERNA_INDEX	sortmerna	`4.3.7`
STAR_ALIGN	gawk	`5.1.0`
	samtools	`1.21`
	star	`2.7.11b`
STAR_GENOMEGENERATE	gawk	`5.1.0`
	samtools	`1.21`
	star	`2.7.11b`
SortMeRNA	sortmerna	`4.3.7`
TXIMETA_TXIMPORT	bioconductor-tximeta	`1.20.1`
UMITOOLS_DEDUP	umitools	`1.1.5`
UMITOOLS_EXTRACT	umitools	`1.1.5`
Workflow	Nextflow	`25.04.7`
	nf-core/rnaseq	`v3.22.2-g3816d48`
fastp	fastp	`0.24.0`

nf-core/rnaseq Methods Description

Suggested text and references to use when describing pipeline usage within the methods section of a publication.https://github.com/nf-core/rnaseq

Methods

Data was processed using nf-core/rnaseq v3.22.2 (doi: 10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v25.04.7 (Di Tommaso et al., 2017) with the following command:

nextflow run nf-core/rnaseq -r 3.22.2 -c ../rnaseq.config -params-file ../params_rnaseq.json -resume -profile crg_slurm

References

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192

Notes:

The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

nf-core/rnaseq Workflow Summary

this information is collected when the pipeline is started.https://github.com/nf-core/rnaseq

Input/output options

input: ../samplesheet_all.csv
multiqc_title: PTox-WP2
outdir: ./rnaseq_output

Reference genome options

fasta: ../refs/Human/genome_with_spikes.fa
gtf: ../refs/Human/genome_annotation_with_spikes.gtf
gtf_extra_attributes: gene

Read trimming options

extra_fastp_args: --length_required=20 --trim_poly_g --poly_g_min_len=20 --trim_poly_x --poly_x_min_len=15 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --dont_eval_duplication --cut_tail
trimmer: fastp

Read filtering options

remove_ribo_rna: true

UMI options

umi_discard_read: 0
umitools_bc_pattern: ^(?P.{6})(?P.{4}).*
umitools_dedup_stats: true
umitools_extract_method: regex
with_umi: true

Alignment options

extra_salmon_quant_args: --noLengthCorrection
extra_star_align_args: --alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA
stranded_threshold: 0.7

Process skipping options

skip_bigwig: true
skip_biotype_qc: true
skip_dupradar: true
skip_preseq: false
skip_pseudo_alignment: true
skip_stringtie: true

Generic options

monochrome_logs: true
trace_report_suffix: 2026-07-13_08-33-16

Core Nextflow options

configFiles: /users/rg/vntasis/.nextflow/assets/nf-core/rnaseq/nextflow.config, /users/project/precisiontox_008279_no_backup/wp2_data/rnaseq_run/../rnaseq.config
containerEngine: apptainer
launchDir: /users/project/precisiontox_008279_no_backup/wp2_data/rnaseq_run
profile: crg_slurm
projectDir: /users/rg/vntasis/.nextflow/assets/nf-core/rnaseq
revision: 3.22.2
runName: elegant_wright
userName: vntasis
workDir: /users/project/precisiontox_008279_no_backup/wp2_data/rnaseq_run/work

PTox-WP2

MultiQC Toolbox

Apply Highlight Samples

Rename Samples Bulk input Apply

Apply Show / Hide Samples

Explain with AI

Export Plots

Choose Plots All None

Save Settings

Load Settings

Tool Citations

About MultiQC

PTox-WP2

Report AI Summary

General Statistics

AI Summary

General Statistics: Columns

Sample status checks

Strandedness Checks

AI Summary

Samples strandedness check: Columns

FastQC (raw)

Sequence Counts Help

AI Summary

AI Summary

AI Summary

Per Base Sequence Content Help

AI Summary

Rollover for sample name

AI Summary

AI Summary

AI Summary

AI Summary

Overrepresented sequences by sample Help

AI Summary

Top overrepresented sequences

AI Summary

FastQC: Top overrepresented sequences: Columns

AI Summary

Status Checks Help

AI Summary

fastp

Filtered Reads

AI Summary

Sequence Quality

AI Summary

GC Content

AI Summary

N content

AI Summary

FastQC (trimmed)

Sequence Counts Help

AI Summary

AI Summary

AI Summary

Per Base Sequence Content Help

AI Summary

Rollover for sample name

AI Summary

AI Summary

AI Summary

AI Summary

Overrepresented sequences by sample Help

AI Summary

Top overrepresented sequences

AI Summary

FastQC: Top overrepresented sequences: Columns

AI Summary

Status Checks Help

AI Summary

Preseq

Complexity curve (molecule count)

AI Summary

QualiMap

Genomic origin of reads Help

AI Summary

Gene Coverage Profile Help

AI Summary

RSeQC

Read Distribution

Highlight Samples

Rename Samples

Show / Hide Samples

Choose Plots

Sequence Counts

Per Base Sequence Content

Overrepresented sequences by sample

Status Checks

Sequence Counts

Per Base Sequence Content

Overrepresented sequences by sample

Status Checks

Genomic origin of reads

Gene Coverage Profile

Percent mapped

UMI Stats