MoP4-g - pipeline: MultiQC Report

General Statistics

Showing ¹³⁰/₁₃₀ rows and ⁷/₁₆ columns.

Sample Name	# Sequences	Total bp	Avg Length	GC%	Q30%	Avg Qual	N50	Reads	Bases	Read N50	Longest Read	Shortest Read	Mean Length	Median Length	Mean Qual	Median Qual
Acas_rep1_ivt								0.0M	1.9Mb	301bp	2810bp	9bp	285.0bp	249	13.7	14.3
Acas_rep1_native								0.0M	1.9Mb	1621bp	5788bp	13bp	447.0bp	156	10.0	10.4
Atha_rep1_ivt								0.0M	1.0Mb	316bp	2318bp	13bp	283.0bp	260	10.2	9.5
Atha_rep1_native								0.0M	1.3Mb	1106bp	3884bp	21bp	388.0bp	147	11.2	11.0
Bnat_rep1_ivt								0.0M	0.4Mb	274bp	3448bp	14bp	227.0bp	210	13.2	14.0
Bnat_rep1_native								0.0M	0.5Mb	470bp	3626bp	17bp	260.0bp	138	9.9	9.8
Cfra_rep1_ivt								0.0M	0.6Mb	317bp	2497bp	9bp	269.0bp	244	13.3	13.8
Cfra_rep1_native								0.0M	1.3Mb	626bp	3641bp	18bp	315.0bp	168	12.9	13.4
Cowc_rep1_ivt								0.0M	0.9Mb	643bp	2085bp	15bp	465.0bp	362	14.0	14.4
Cowc_rep1_native								0.0M	5.8Mb	1792bp	6078bp	17bp	935.0bp	840	14.6	14.6
Ddis_rep1_ivt								0.0M	1.9Mb	287bp	5194bp	5bp	263.0bp	217	13.9	14.6
Ddis_rep1_native								0.0M	6.5Mb	1887bp	8461bp	15bp	681.0bp	163	15.8	16.4
Gthe_rep1_ivt								0.0M	1.5Mb	296bp	6592bp	6bp	244.0bp	200	13.2	13.7
Gthe_rep1_native								0.0M	0.7Mb	807bp	3393bp	18bp	304.0bp	155	9.7	9.5
Hsap_rep1_ivt								0.0M	1.5Mb	292bp	3605bp	11bp	256.0bp	258	12.6	13.2
Hsap_rep1_native								0.0M	2.4Mb	1598bp	7858bp	15bp	552.0bp	190	11.1	11.6
Itha_rep1_ivt								0.0M	0.7Mb	357bp	7229bp	11bp	267.0bp	191	9.8	9.3
Itha_rep1_native								0.0M	0.9Mb	746bp	3683bp	11bp	310.0bp	150	10.4	9.9
Mlei_rep1_ivt								0.0M	1.7Mb	396bp	2604bp	15bp	370.0bp	322	11.5	11.4
Mlei_rep1_native								0.0M	2.3Mb	1839bp	4804bp	16bp	541.0bp	196	10.7	10.9
Mmus_rep1_ivt								0.0M	1.7Mb	282bp	2676bp	12bp	235.0bp	239	12.6	13.1
Mmus_rep1_native								0.0M	3.4Mb	1498bp	6063bp	18bp	659.0bp	247	12.3	12.6
Mpol_rep1_ivt								0.0M	1.2Mb	354bp	3516bp	12bp	298.0bp	257	13.0	13.6
Mpol_rep1_native								0.0M	1.3Mb	1475bp	4045bp	21bp	566.0bp	182	11.5	11.8
Ngru_rep1_ivt								0.0M	2.6Mb	505bp	5716bp	14bp	383.0bp	300	13.6	14.2
Ngru_rep1_native								0.0M	4.1Mb	1346bp	6466bp	18bp	520.0bp	168	12.8	13.3
Nvec_rep1_ivt								0.0M	0.3Mb	277bp	2234bp	11bp	225.0bp	224	12.2	12.8
Nvec_rep1_native								0.0M	1.9Mb	567bp	5496bp	13bp	254.0bp	122	10.2	10.4
Scer_rep1_ivt								0.0M	1.1Mb	232bp	2674bp	10bp	220.0bp	203	13.8	14.4
Scer_rep1_native								0.0M	1.1Mb	539bp	5363bp	19bp	214.0bp	96	10.4	9.3
Scin_rep1_ivt								0.0M	1.0Mb	432bp	2699bp	16bp	361.0bp	309	10.1	10.2
Scin_rep1_native								0.0M	2.4Mb	1832bp	6435bp	10bp	571.0bp	192	10.9	11.4
Skew_rep1_ivt								0.0M	1.0Mb	351bp	3377bp	8bp	300.0bp	271	12.2	12.6
Skew_rep1_native								0.0M	0.5Mb	643bp	3641bp	21bp	350.0bp	187	11.6	11.7
Smic_rep1_ivt								0.0M	1.2Mb	400bp	3124bp	17bp	323.0bp	280	12.2	12.3
Smic_rep1_native								0.0M	0.9Mb	555bp	7878bp	13bp	334.0bp	189	11.9	12.1
Spun_rep1_ivt								0.0M	0.7Mb	365bp	2013bp	22bp	290.0bp	242	11.2	11.2
Spun_rep1_native								0.0M	1.5Mb	1596bp	4565bp	10bp	568.0bp	207	12.4	13.2
Tthe_rep1_ivt								0.0M	0.9Mb	339bp	2114bp	20bp	302.0bp	281	10.9	10.7
Tthe_rep1_native								0.0M	1.0Mb	138bp	4981bp	19bp	125.0bp	89	7.7	7.4
pod5---bc_1	0.0M	1.9Mb	447.7bp	49.0%	14.3%	10.8	1621bp
pod5---bc_2	0.0M	1.3Mb	388.8bp	48.6%	35.0%	11.9	1106bp
pod5---bc_3	0.0M	0.5Mb	260.8bp	41.2%	19.4%	10.0	470bp
pod5---bc_4	0.0M	5.8Mb	935.3bp	46.4%	31.4%	13.7	1792bp
pod5---bc_5	0.0M	1.3Mb	315.5bp	41.5%	26.2%	13.4	626bp
pod5---bc_6	0.0M	6.5Mb	681.8bp	42.0%	33.5%	14.8	1887bp
pod5---bc_7	0.0M	0.5Mb	350.7bp	41.5%	20.6%	11.1	643bp
pod5---bc_8	0.0M	0.7Mb	304.1bp	43.4%	19.4%	10.5	807bp
pod5---bc_9	0.0M	1.3Mb	566.3bp	48.0%	24.6%	11.7	1475bp
pod5---bc_10	0.0M	4.1Mb	520.8bp	44.6%	22.3%	13.5	1346bp
pod5---bc_11	0.0M	1.9Mb	254.8bp	43.8%	17.3%	10.6	567bp
pod5---bc_12	0.0M	1.1Mb	214.4bp	43.1%	23.1%	11.6	539bp
pod5---bc_13	0.0M	1.5Mb	568.3bp	43.7%	26.7%	12.9	1596bp
pod5---bc_14	0.0M	0.9Mb	334.2bp	41.7%	20.0%	11.3	555bp
pod5---bc_15	0.0M	1.0Mb	125.9bp	38.2%	10.5%	7.6	138bp
pod5---bc_16	0.0M	2.3Mb	541.1bp	45.9%	21.0%	11.7	1839bp
pod5---bc_17	0.0M	3.4Mb	659.8bp	54.2%	18.4%	12.1	1498bp
pod5---bc_18	0.0M	2.4Mb	552.9bp	55.3%	17.2%	11.1	1598bp
pod5---bc_19	0.0M	0.9Mb	310.8bp	46.3%	26.2%	10.8	746bp
pod5---bc_20	0.0M	2.4Mb	571.3bp	44.6%	27.6%	12.2	1832bp
pod5---bc_21	0.0M	1.9Mb	285.3bp	41.5%	22.9%	12.7	301bp
pod5---bc_22	0.0M	1.0Mb	283.2bp	39.2%	28.9%	9.6	316bp
pod5---bc_23	0.0M	0.4Mb	227.6bp	36.2%	22.7%	11.9	274bp
pod5---bc_24	0.0M	0.9Mb	465.1bp	39.9%	39.8%	13.4	643bp
pod5---bc_25	0.0M	0.6Mb	269.1bp	37.2%	32.0%	12.5	317bp
pod5---bc_26	0.0M	1.9Mb	263.7bp	34.5%	25.5%	13.2	287bp
pod5---bc_27	0.0M	1.0Mb	300.7bp	35.9%	34.8%	11.7	351bp
pod5---bc_28	0.0M	1.5Mb	244.8bp	36.6%	28.6%	12.3	296bp
pod5---bc_29	0.0M	1.2Mb	299.0bp	38.9%	30.6%	12.2	354bp
pod5---bc_30	0.0M	2.6Mb	383.9bp	38.1%	31.5%	13.2	505bp
pod5---bc_31	0.0M	0.3Mb	225.4bp	35.4%	21.2%	11.6	277bp
pod5---bc_32	0.0M	1.1Mb	220.1bp	38.1%	22.8%	13.2	232bp
pod5---bc_33	0.0M	0.7Mb	290.7bp	35.2%	30.6%	10.8	365bp
pod5---bc_34	0.0M	1.2Mb	323.1bp	38.0%	35.6%	11.9	400bp
pod5---bc_35	0.0M	0.9Mb	302.0bp	32.9%	29.5%	10.6	339bp
pod5---bc_36	0.0M	1.7Mb	370.0bp	38.8%	28.3%	11.2	396bp
pod5---bc_37	0.0M	1.7Mb	235.1bp	36.7%	22.6%	12.2	282bp
pod5---bc_38	0.0M	1.5Mb	256.3bp	38.8%	19.5%	11.9	292bp
pod5---bc_39	0.0M	0.7Mb	267.2bp	40.3%	19.3%	9.7	357bp
pod5---bc_40	0.0M	1.0Mb	362.0bp	38.2%	29.4%	10.3	432bp
pod5---bc_41	0.0M	0.0Mb	291.0bp	37.1%	19.2%	16.3	291bp
pod5---bc_43	0.0M	0.0Mb	397.2bp	44.9%	8.9%	9.5	930bp
pod5---bc_44	0.0M	0.0Mb	105.0bp	41.9%	3.8%	8.0	166bp
pod5---bc_45	0.0M	0.0Mb	383.8bp	52.7%	27.8%	11.0	1303bp
pod5---bc_46	0.0M	0.0Mb	122.9bp	35.6%	14.3%	8.3	195bp
pod5---bc_47	0.0M	0.0Mb	208.6bp	41.8%	10.6%	8.6	261bp
pod5---bc_48	0.0M	0.0Mb	111.6bp	42.0%	15.9%	7.5	179bp
pod5---bc_49	0.0M	0.0Mb	288.7bp	41.7%	32.8%	10.1	759bp
pod5---bc_50	0.0M	0.0Mb	123.3bp	37.9%	16.2%	7.5	143bp
pod5---bc_51	0.0M	0.0Mb	477.7bp	43.4%	26.1%	13.1	1980bp
pod5---bc_52	0.0M	0.0Mb	420.8bp	39.8%	28.1%	10.8	1290bp
pod5---bc_53	0.0M	0.0Mb	281.7bp	43.3%	13.2%	10.9	294bp
pod5---bc_54	0.0M	0.0Mb	564.4bp	47.6%	16.2%	12.7	1854bp
pod5---bc_55	0.0M	0.0Mb	268.5bp	36.2%	12.6%	8.6	335bp
pod5---bc_56	0.0M	0.0Mb	160.3bp	36.8%	20.6%	12.3	295bp
pod5---bc_57	0.0M	0.0Mb	637.3bp	44.3%	28.2%	12.4	887bp
pod5---bc_58	0.0M	0.0Mb	157.8bp	36.8%	19.0%	7.6	214bp
pod5---bc_59	0.0M	0.0Mb	368.2bp	42.9%	17.4%	11.4	665bp
pod5---bc_60	0.0M	0.0Mb	395.4bp	42.0%	12.9%	11.8	1843bp
pod5---bc_61	0.0M	0.0Mb	118.8bp	37.5%	2.9%	6.8	133bp
pod5---bc_62	0.0M	0.0Mb	833.5bp	58.9%	7.6%	7.8	6932bp
pod5---bc_63	0.0M	0.0Mb	87.8bp	35.0%	1.4%	6.5	94bp
pod5---bc_65	0.0M	0.0Mb	282.0bp	39.2%	17.9%	9.6	364bp
pod5---bc_66	0.0M	0.0Mb	352.0bp	43.8%	35.2%	15.8	352bp
pod5---bc_68	0.0M	0.0Mb	168.0bp	28.6%	20.5%	10.4	206bp
pod5---bc_69	0.0M	0.0Mb	74.0bp	47.3%	0.0%	5.5	74bp
pod5---bc_71	0.0M	0.0Mb	134.5bp	37.9%	0.4%	11.3	174bp
pod5---bc_72	0.0M	0.0Mb	718.3bp	41.7%	29.0%	14.6	1829bp
pod5---bc_73	0.0M	0.0Mb	60.0bp	18.3%	0.0%	13.1	60bp
pod5---bc_74	0.0M	0.0Mb	399.0bp	40.9%	16.0%	12.4	399bp
pod5---bc_75	0.0M	0.0Mb	358.1bp	44.4%	20.0%	12.2	680bp
pod5---bc_76	0.0M	0.0Mb	276.0bp	42.6%	43.9%	13.4	760bp
pod5---bc_77	0.0M	0.0Mb	627.0bp	42.3%	36.0%	11.8	1680bp
pod5---bc_78	0.0M	0.0Mb	144.8bp	34.8%	4.4%	6.4	192bp
pod5---bc_79	0.0M	0.0Mb	209.7bp	33.0%	27.0%	12.2	246bp
pod5---bc_80	0.0M	0.0Mb	351.3bp	41.5%	28.3%	14.3	959bp
pod5---bc_81	0.0M	0.0Mb	212.5bp	35.3%	29.3%	13.4	240bp
pod5---bc_82	0.0M	0.0Mb	200.0bp	43.2%	9.5%	9.3	257bp
pod5---bc_83	0.0M	0.0Mb	184.0bp	46.2%	15.2%	9.7	184bp
pod5---bc_84	0.0M	0.0Mb	221.5bp	32.0%	17.6%	12.2	277bp
pod5---bc_85	0.0M	0.0Mb	143.7bp	35.3%	14.6%	10.6	268bp
pod5---bc_86	0.0M	0.0Mb	359.8bp	42.6%	17.8%	11.3	396bp
pod5---bc_87	0.0M	0.0Mb	621.5bp	43.1%	45.9%	11.5	629bp
pod5---bc_88	0.0M	0.0Mb	277.0bp	47.3%	47.6%	18.8	277bp
pod5---bc_89	0.0M	0.0Mb	61.9bp	35.6%	0.0%	3.8	56bp
pod5---bc_91	0.0M	0.0Mb	605.0bp	41.5%	55.5%	13.4	605bp
pod5---bc_92	0.0M	0.0Mb	266.9bp	39.6%	22.2%	10.0	282bp
pod5---bc_93	0.0M	0.0Mb	171.7bp	40.4%	19.7%	9.7	726bp
pod5---bc_94	0.0M	0.0Mb	63.0bp	49.2%	0.0%	5.6	72bp
pod5---bc_95	0.0M	0.0Mb	280.8bp	36.2%	15.8%	9.5	405bp

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
\|\|	SeqKit: seqkit	# Sequences	Number of sequences (millions)	`seqkit_seqkit-num_seqs`	read_count
\|\|	SeqKit: seqkit	Total bp	Total number of bases (millions)	`seqkit_seqkit-sum_len`	base_count
\|\|	SeqKit: seqkit	Avg Length	Average sequence length	`seqkit_seqkit-avg_len`
\|\|	SeqKit: seqkit	GC%	GC content percentage	`seqkit_seqkit-GC_pct`
\|\|	SeqKit: seqkit	Q30%	Percentage of bases with quality score >= 30	`seqkit_seqkit-Q30_pct`
\|\|	SeqKit: seqkit	Avg Qual	Average quality score	`seqkit_seqkit-AvgQual`
\|\|	SeqKit: seqkit	N50	N50 sequence length	`seqkit_seqkit-N50`
\|\|	Nanoq	Reads	Number of reads	`Number_of_reads`	read_count
\|\|	Nanoq	Bases	Total bases sequenced	`Number_of_bases`	base_count
\|\|	Nanoq	Read N50	N50 read length	`N50_read_length`
\|\|	Nanoq	Longest Read	Longest read length	`Longest_read`
\|\|	Nanoq	Shortest Read	Shortest read length	`Shortest_read`
\|\|	Nanoq	Mean Length	Mean read length	`Mean_read_length`
\|\|	Nanoq	Median Length	Median read length (bp)	`Median_read_length`
\|\|	Nanoq	Mean Qual	Mean read quality (Phred scale)	`Mean_read_quality`
\|\|	Nanoq	Median Qual	Median read quality (Phred scale)	`Median_read_quality`

Alignment QC

Showing ⁴⁰/₄₀ rows and ⁷/₇ columns.

File name	Mapped reads	Map %	Bases	Bases %	Avg read length	Max read length	identity
Acas_rep1_ivt_s.cram	1509	22.5%	507142	26.5%	285	2810	96.47%
Acas_rep1_native_s.cram	1004	23.6%	1252156	65.7%	447	5788	94.29%
Atha_rep1_ivt_s.cram	454	12.8%	100642	10.0%	283	2318	95.07%
Atha_rep1_native_s.cram	938	29.0%	602401	48.0%	388	3884	88.99%
Bnat_rep1_ivt_s.cram	213	10.8%	51509	11.5%	227	3448	86.96%
Bnat_rep1_native_s.cram	376	18.9%	189166	36.4%	260	3626	84.87%
Cfra_rep1_ivt_s.cram	933	42.9%	210992	36.0%	269	2497	91.97%
Cfra_rep1_native_s.cram	2277	56.4%	907570	71.3%	315	3641	89.55%
Cowc_rep1_ivt_s.cram	1029	53.3%	457681	51.0%	465	2085	92.92%
Cowc_rep1_native_s.cram	3512	57.1%	4541693	78.9%	935	6078	94.99%
Ddis_rep1_ivt_s.cram	799	11.0%	364155	19.0%	263	5194	96.78%
Ddis_rep1_native_s.cram	2708	28.4%	4756104	73.2%	681	8461	95.96%
Gthe_rep1_ivt_s.cram	858	14.0%	238847	15.9%	244	6592	81.41%
Gthe_rep1_native_s.cram	388	17.3%	279629	41.1%	304	3393	80.40%
Hsap_rep1_ivt_s.cram	3384	56.6%	532359	34.8%	256	3605	97.77%
Hsap_rep1_native_s.cram	2630	60.0%	1947376	80.4%	552	7858	92.37%
Itha_rep1_ivt_s.cram	794	29.9%	273695	38.6%	267	7229	92.83%
Itha_rep1_native_s.cram	740	26.0%	390195	44.0%	310	3683	86.84%
Mlei_rep1_ivt_s.cram	1770	38.9%	541428	32.2%	370	2604	93.17%
Mlei_rep1_native_s.cram	1488	35.4%	1500721	66.0%	541	4804	94.68%
Mmus_rep1_ivt_s.cram	2769	37.5%	428852	24.7%	235	2676	96.98%
Mmus_rep1_native_s.cram	3512	67.9%	2756520	80.8%	659	6063	92.17%
Mpol_rep1_ivt_s.cram	1049	25.9%	288588	23.9%	298	3516	90.83%
Mpol_rep1_native_s.cram	731	30.8%	810048	60.3%	566	4045	86.01%
Ngru_rep1_ivt_s.cram	3899	57.8%	1386035	53.5%	383	5716	97.61%
Ngru_rep1_native_s.cram	3330	42.2%	3199252	77.9%	520	6466	95.89%
Nvec_rep1_ivt_s.cram	366	23.6%	57443	16.4%	225	2234	97.51%
Nvec_rep1_native_s.cram	1179	16.0%	883349	47.1%	254	5496	95.05%
Scer_rep1_ivt_s.cram	1506	31.0%	274086	25.7%	220	2674	98.96%
Scer_rep1_native_s.cram	1829	34.3%	718155	62.8%	214	5363	97.45%
Scin_rep1_ivt_s.cram	1000	37.8%	349232	36.5%	361	2699	89.18%
Scin_rep1_native_s.cram	2000	47.4%	1916428	79.5%	571	6435	87.43%
Skew_rep1_ivt_s.cram	580	16.9%	192079	18.6%	300	3377	95.70%
Skew_rep1_native_s.cram	335	23.0%	203389	39.8%	350	3641	90.53%
Smic_rep1_ivt_s.cram	935	25.3%	313429	26.2%	323	3124	96.38%
Smic_rep1_native_s.cram	707	27.6%	392729	45.9%	334	7878	91.54%
Spun_rep1_ivt_s.cram	580	24.0%	193727	27.6%	290	2013	83.88%
Spun_rep1_native_s.cram	1051	40.2%	909855	61.2%	568	4565	92.70%
Tthe_rep1_ivt_s.cram	654	21.6%	224566	24.5%	302	2114	97.39%
Tthe_rep1_native_s.cram	219	2.7%	112637	11.1%	125	4981	97.01%

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: alnQC-section-plot_table

Sort	Column	Description	ID
\|\|	Mapped reads	Mapped reads	`Mapped_reads`
\|\|	Map %	Map %	`Map`
\|\|	Bases	Bases	`Bases`
\|\|	Bases %	Bases %	`Bases-1`
\|\|	Avg read length	Avg read length	`Avg_read_length`
\|\|	Max read length	Max read length	`Max_read_length`
\|\|	identity	identity	`identity`

Nanoq

This section of the report shows statistics on read quality and length from nanopore sequencing data.https://github.com/nerdna/nanoqDOI: 10.21105/joss.02991

Nanoq Summary

Statistics from Nanoq reports

Showing ⁴⁰/₄₀ rows and ⁹/₉ columns.

Sample Name	Reads	Bases	Read N50	Longest Read	Shortest Read	Mean Length	Median Length	Mean Qual	Median Qual
Acas_rep1_ivt	0.0M	1.9Mb	301bp	2810bp	9bp	285.0bp	249	13.7	14.3
Acas_rep1_native	0.0M	1.9Mb	1621bp	5788bp	13bp	447.0bp	156	10.0	10.4
Atha_rep1_ivt	0.0M	1.0Mb	316bp	2318bp	13bp	283.0bp	260	10.2	9.5
Atha_rep1_native	0.0M	1.3Mb	1106bp	3884bp	21bp	388.0bp	147	11.2	11.0
Bnat_rep1_ivt	0.0M	0.4Mb	274bp	3448bp	14bp	227.0bp	210	13.2	14.0
Bnat_rep1_native	0.0M	0.5Mb	470bp	3626bp	17bp	260.0bp	138	9.9	9.8
Cfra_rep1_ivt	0.0M	0.6Mb	317bp	2497bp	9bp	269.0bp	244	13.3	13.8
Cfra_rep1_native	0.0M	1.3Mb	626bp	3641bp	18bp	315.0bp	168	12.9	13.4
Cowc_rep1_ivt	0.0M	0.9Mb	643bp	2085bp	15bp	465.0bp	362	14.0	14.4
Cowc_rep1_native	0.0M	5.8Mb	1792bp	6078bp	17bp	935.0bp	840	14.6	14.6
Ddis_rep1_ivt	0.0M	1.9Mb	287bp	5194bp	5bp	263.0bp	217	13.9	14.6
Ddis_rep1_native	0.0M	6.5Mb	1887bp	8461bp	15bp	681.0bp	163	15.8	16.4
Gthe_rep1_ivt	0.0M	1.5Mb	296bp	6592bp	6bp	244.0bp	200	13.2	13.7
Gthe_rep1_native	0.0M	0.7Mb	807bp	3393bp	18bp	304.0bp	155	9.7	9.5
Hsap_rep1_ivt	0.0M	1.5Mb	292bp	3605bp	11bp	256.0bp	258	12.6	13.2
Hsap_rep1_native	0.0M	2.4Mb	1598bp	7858bp	15bp	552.0bp	190	11.1	11.6
Itha_rep1_ivt	0.0M	0.7Mb	357bp	7229bp	11bp	267.0bp	191	9.8	9.3
Itha_rep1_native	0.0M	0.9Mb	746bp	3683bp	11bp	310.0bp	150	10.4	9.9
Mlei_rep1_ivt	0.0M	1.7Mb	396bp	2604bp	15bp	370.0bp	322	11.5	11.4
Mlei_rep1_native	0.0M	2.3Mb	1839bp	4804bp	16bp	541.0bp	196	10.7	10.9
Mmus_rep1_ivt	0.0M	1.7Mb	282bp	2676bp	12bp	235.0bp	239	12.6	13.1
Mmus_rep1_native	0.0M	3.4Mb	1498bp	6063bp	18bp	659.0bp	247	12.3	12.6
Mpol_rep1_ivt	0.0M	1.2Mb	354bp	3516bp	12bp	298.0bp	257	13.0	13.6
Mpol_rep1_native	0.0M	1.3Mb	1475bp	4045bp	21bp	566.0bp	182	11.5	11.8
Ngru_rep1_ivt	0.0M	2.6Mb	505bp	5716bp	14bp	383.0bp	300	13.6	14.2
Ngru_rep1_native	0.0M	4.1Mb	1346bp	6466bp	18bp	520.0bp	168	12.8	13.3
Nvec_rep1_ivt	0.0M	0.3Mb	277bp	2234bp	11bp	225.0bp	224	12.2	12.8
Nvec_rep1_native	0.0M	1.9Mb	567bp	5496bp	13bp	254.0bp	122	10.2	10.4
Scer_rep1_ivt	0.0M	1.1Mb	232bp	2674bp	10bp	220.0bp	203	13.8	14.4
Scer_rep1_native	0.0M	1.1Mb	539bp	5363bp	19bp	214.0bp	96	10.4	9.3
Scin_rep1_ivt	0.0M	1.0Mb	432bp	2699bp	16bp	361.0bp	309	10.1	10.2
Scin_rep1_native	0.0M	2.4Mb	1832bp	6435bp	10bp	571.0bp	192	10.9	11.4
Skew_rep1_ivt	0.0M	1.0Mb	351bp	3377bp	8bp	300.0bp	271	12.2	12.6
Skew_rep1_native	0.0M	0.5Mb	643bp	3641bp	21bp	350.0bp	187	11.6	11.7
Smic_rep1_ivt	0.0M	1.2Mb	400bp	3124bp	17bp	323.0bp	280	12.2	12.3
Smic_rep1_native	0.0M	0.9Mb	555bp	7878bp	13bp	334.0bp	189	11.9	12.1
Spun_rep1_ivt	0.0M	0.7Mb	365bp	2013bp	22bp	290.0bp	242	11.2	11.2
Spun_rep1_native	0.0M	1.5Mb	1596bp	4565bp	10bp	568.0bp	207	12.4	13.2
Tthe_rep1_ivt	0.0M	0.9Mb	339bp	2114bp	20bp	302.0bp	281	10.9	10.7
Tthe_rep1_native	0.0M	1.0Mb	138bp	4981bp	19bp	125.0bp	89	7.7	7.4

Expand table

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

Sort	Column	Description	ID	Scale
\|\|	Reads	Number of reads	`Number_of_reads`	read_count
\|\|	Bases	Total bases sequenced	`Number_of_bases`	base_count
\|\|	Read N50	N50 read length	`N50_read_length`
\|\|	Longest Read	Longest read length	`Longest_read`
\|\|	Shortest Read	Shortest read length	`Shortest_read`
\|\|	Mean Length	Mean read length	`Mean_read_length`
\|\|	Median Length	Median read length (bp)	`Median_read_length`
\|\|	Mean Qual	Mean read quality (Phred scale)	`Mean_read_quality`
\|\|	Median Qual	Median read quality (Phred scale)	`Median_read_quality`

Read quality

Read counts categorised by read quality (Phred score).

Sequencing machines assign each generated read a quality score using the Phred scale. The phred score represents the liklelyhood that a given read contains errors. High quality reads have a high score.

Created with MultiQC

Read lengths

Read counts categorised by read length.

Created with MultiQC

Methods Description

Basecalling of raw nanopore signal data was performed using Dorado version 1.4.0 with parameters sup@v5.3.0,pseU_2OmeU [1].

Demultiplexing of raw nanopore signal data was carried out using SeqTagger version 1.1a with parameters -k b96_RNA004 [2].

Read filtering of raw nanopore signal data was performed using SeqKit version 2.9.0 [3].

Read filtering and QC statistics were obtained using Nanoq version 0.10.0 [4].

Filtered reads were aligned to the reference genome multi_species using Minimap2 version 2.29-r1283 with parameters -y -uf -k14 [5].

Aligned reads were sorted and indexed using Samtools version 1.22.1 [6].

Citations

https://github.com/nanoporetech/dorado
Pryszcz, L. P., Diensthuber, G., Llovera, L., Medina, R., Delgado-Tejedor, A., Cozzuto, L., Ponomarenko, J., & Novoa, E. M. (2025). Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger. _Genome Research_, _35_(4), 956–966. https://doi.org/10.1101/gr.279290.124
Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. _PLOS ONE_, _11_(10), e0163962. https://doi.org/10.1371/journal.pone.0163962
Steinig, E., & Coin, L. (2022). Nanoq: ultra-fast quality control for nanopore reads. _Journal of Open Source Software_, _7_(69), 2991. https://doi.org/10.21105/joss.02991
https://github.com/lh3/minimap2
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. _Bioinformatics_, _25_(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352

SeqKit

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation.https://bioinf.shenwei.me/seqkitDOI: 10.1371/journal.pone.0163962

Stats

Statistics from seqkit stats showing sequence file metrics.

Showing ⁹⁰/₉₀ rows and ¹⁴/₁₈ columns.

Sample Name	Format	Type	# Seqs	Total Length	Min Length	Avg Length	Q1 Length	Median Length	Q3 Length	Max Length	N50	N50 Count	Q20%	Q30%	Avg Quality	GC%
pod5---bc_1	FASTQ	DNA	0.0M	1.9Mb	13	447.7	113	156	288	5788	1621	311	61.2%	14.3%	10.8	49.0%
pod5---bc_2	FASTQ	DNA	0.0M	1.3Mb	21	388.8	105	147	351	3884	1106	285	70.4%	35.0%	11.9	48.6%
pod5---bc_3	FASTQ	DNA	0.0M	0.5Mb	17	260.8	88	138	242	3626	470	207	57.7%	19.4%	10.0	41.2%
pod5---bc_4	FASTQ	DNA	0.0M	5.8Mb	17	935.3	171	840	1792	6078	1792	250	74.8%	31.4%	13.7	46.4%
pod5---bc_5	FASTQ	DNA	0.0M	1.3Mb	18	315.5	99	168	312	3641	626	395	71.7%	26.2%	13.4	41.5%
pod5---bc_6	FASTQ	DNA	0.0M	6.5Mb	15	681.8	134	163	733	8461	1887	649	78.8%	33.5%	14.8	42.0%
pod5---bc_7	FASTQ	DNA	0.0M	0.5Mb	21	350.7	131	187	364	3641	643	194	59.8%	20.6%	11.1	41.5%
pod5---bc_8	FASTQ	DNA	0.0M	0.7Mb	18	304.1	85	156	236	3393	807	201	58.5%	19.4%	10.5	43.4%
pod5---bc_9	FASTQ	DNA	0.0M	1.3Mb	21	566.3	136	182	796	4045	1475	264	64.4%	24.6%	11.7	48.0%
pod5---bc_10	FASTQ	DNA	0.0M	4.1Mb	18	520.8	114	168	597	6466	1346	556	72.0%	22.3%	13.5	44.6%
pod5---bc_11	FASTQ	DNA	0.0M	1.9Mb	13	254.8	87	122	215	5496	567	520	59.0%	17.3%	10.6	43.8%
pod5---bc_12	FASTQ	DNA	0.0M	1.1Mb	19	214.4	79	96	166	5363	539	292	65.8%	23.1%	11.6	43.1%
pod5---bc_13	FASTQ	DNA	0.0M	1.5Mb	10	568.3	133	207	646	4565	1596	237	70.5%	26.7%	12.9	43.7%
pod5---bc_14	FASTQ	DNA	0.0M	0.9Mb	13	334.2	125	189	349	7878	555	316	60.7%	20.0%	11.3	41.7%
pod5---bc_15	FASTQ	DNA	0.0M	1.0Mb	19	125.9	75	89	128	4981	138	328	37.9%	10.5%	7.6	38.2%
pod5---bc_16	FASTQ	DNA	0.0M	2.3Mb	16	541.1	120	196	426	4804	1839	264	65.1%	21.0%	11.7	45.9%
pod5---bc_17	FASTQ	DNA	0.0M	3.4Mb	18	659.8	164	247	896	6063	1498	519	65.0%	18.4%	12.1	54.2%
pod5---bc_18	FASTQ	DNA	0.0M	2.4Mb	15	552.9	119	190	644	7858	1598	360	62.0%	17.2%	11.1	55.3%
pod5---bc_19	FASTQ	DNA	0.0M	0.9Mb	11	310.8	85	150	274	3683	746	270	62.7%	26.2%	10.8	46.3%
pod5---bc_20	FASTQ	DNA	0.0M	2.4Mb	10	571.3	86	192	725	6435	1832	301	69.1%	27.6%	12.2	44.6%
pod5---bc_21	FASTQ	DNA	0.0M	1.9Mb	9	285.3	182	249	310	2810	301	583	72.3%	22.9%	12.7	41.5%
pod5---bc_22	FASTQ	DNA	0.0M	1.0Mb	13	283.2	174	260	329	2318	316	372	57.9%	28.9%	9.6	39.2%
pod5---bc_23	FASTQ	DNA	0.0M	0.4Mb	14	227.6	128	210	284	3448	274	232	67.8%	22.7%	11.9	36.2%
pod5---bc_24	FASTQ	DNA	0.0M	0.9Mb	15	465.1	211	362	632	2085	643	342	75.1%	39.8%	13.4	39.9%
pod5---bc_25	FASTQ	DNA	0.0M	0.6Mb	9	269.1	152	244	325	2497	317	303	71.2%	32.0%	12.5	37.2%
pod5---bc_26	FASTQ	DNA	0.0M	1.9Mb	5	263.7	152	217	288	5194	287	623	72.7%	25.5%	13.2	34.5%
pod5---bc_27	FASTQ	DNA	0.0M	1.0Mb	8	300.7	168	271	361	3377	351	414	67.7%	34.8%	11.7	35.9%
pod5---bc_28	FASTQ	DNA	0.0M	1.5Mb	6	244.8	137	200	304	6592	296	456	69.2%	28.6%	12.3	36.6%
pod5---bc_29	FASTQ	DNA	0.0M	1.2Mb	12	299.0	174	257	363	3516	354	453	69.3%	30.6%	12.2	38.9%
pod5---bc_30	FASTQ	DNA	0.0M	2.6Mb	14	383.9	202	300	484	5716	505	700	73.7%	31.5%	13.2	38.1%
pod5---bc_31	FASTQ	DNA	0.0M	0.3Mb	11	225.4	143	224	298	2234	277	188	65.3%	21.2%	11.6	35.4%
pod5---bc_32	FASTQ	DNA	0.0M	1.1Mb	10	220.1	158	203	256	2674	232	341	71.3%	22.8%	13.2	38.1%
pod5---bc_33	FASTQ	DNA	0.0M	0.7Mb	22	290.7	150	242	359	2013	365	351	63.0%	30.6%	10.8	35.2%
pod5---bc_34	FASTQ	DNA	0.0M	1.2Mb	17	323.1	157	280	391	3124	400	494	69.2%	35.6%	11.9	38.0%
pod5---bc_35	FASTQ	DNA	0.0M	0.9Mb	20	302.0	182	281	351	2114	339	360	64.2%	29.5%	10.6	32.9%
pod5---bc_36	FASTQ	DNA	0.0M	1.7Mb	15	370.0	239	322	416	2604	396	580	67.5%	28.3%	11.2	38.8%
pod5---bc_37	FASTQ	DNA	0.0M	1.7Mb	12	235.1	163	239	297	2676	282	355	66.8%	22.6%	12.2	36.7%
pod5---bc_38	FASTQ	DNA	0.0M	1.5Mb	11	256.3	176	258	309	3605	292	386	67.2%	19.5%	11.9	38.8%
pod5---bc_39	FASTQ	DNA	0.0M	0.7Mb	11	267.2	80	191	314	7229	357	332	56.0%	19.3%	9.7	40.3%
pod5---bc_40	FASTQ	DNA	0.0M	1.0Mb	16	362.0	198	309	434	2699	432	409	59.9%	29.4%	10.3	38.2%
pod5---bc_41	FASTQ	DNA	0.0M	0.0Mb	291	291.0	291	291	291	291	291	1	66.0%	19.2%	16.3	37.1%
pod5---bc_43	FASTQ	DNA	0.0M	0.0Mb	65	397.2	98	149	243	2433	930	2	50.5%	8.9%	9.5	44.9%
pod5---bc_44	FASTQ	DNA	0.0M	0.0Mb	59	105.0	74	90	128	166	166	1	33.0%	3.8%	8.0	41.9%
pod5---bc_45	FASTQ	DNA	0.0M	0.0Mb	50	383.8	86	123	203	2251	1303	2	61.5%	27.8%	11.0	52.7%
pod5---bc_46	FASTQ	DNA	0.0M	0.0Mb	52	122.9	60	70	196	281	195	3	36.8%	14.3%	8.3	35.6%
pod5---bc_47	FASTQ	DNA	0.0M	0.0Mb	37	208.6	82	100	171	1939	261	10	41.9%	10.6%	8.6	41.8%
pod5---bc_48	FASTQ	DNA	0.0M	0.0Mb	28	111.6	57	70	159	326	179	6	43.3%	15.9%	7.5	42.0%
pod5---bc_49	FASTQ	DNA	0.0M	0.0Mb	23	288.7	70	120	234	1891	759	2	62.3%	32.8%	10.1	41.7%
pod5---bc_50	FASTQ	DNA	0.0M	0.0Mb	91	123.3	102	128	145	147	143	2	43.4%	16.2%	7.5	37.9%
pod5---bc_51	FASTQ	DNA	0.0M	0.0Mb	60	477.7	146	248	305	3492	1980	4	72.5%	26.1%	13.1	43.4%
pod5---bc_52	FASTQ	DNA	0.0M	0.0Mb	65	420.8	90	138	774	1298	1290	2	60.4%	28.1%	10.8	39.8%
pod5---bc_53	FASTQ	DNA	0.0M	0.0Mb	75	281.7	117	163	236	1901	294	2	53.3%	13.2%	10.9	43.3%
pod5---bc_54	FASTQ	DNA	0.0M	0.0Mb	64	564.4	105	224	575	1854	1854	1	69.5%	16.2%	12.7	47.6%
pod5---bc_55	FASTQ	DNA	0.0M	0.0Mb	80	268.5	149	185	401	598	335	3	39.2%	12.6%	8.6	36.2%
pod5---bc_56	FASTQ	DNA	0.0M	0.0Mb	66	160.3	93	120	208	295	295	1	58.0%	20.6%	12.3	36.8%
pod5---bc_57	FASTQ	DNA	0.0M	0.0Mb	171	637.3	181	378	887	1830	887	2	67.7%	28.2%	12.4	44.3%
pod5---bc_58	FASTQ	DNA	0.0M	0.0Mb	49	157.8	113	172	214	241	214	2	44.7%	19.0%	7.6	36.8%
pod5---bc_59	FASTQ	DNA	0.0M	0.0Mb	60	368.2	198	274	665	838	665	3	63.1%	17.4%	11.4	42.9%
pod5---bc_60	FASTQ	DNA	0.0M	0.0Mb	65	395.4	77	214	246	1843	1843	1	70.7%	12.9%	11.8	42.0%
pod5---bc_61	FASTQ	DNA	0.0M	0.0Mb	56	118.8	102	121	133	182	133	2	16.8%	2.9%	6.8	37.5%
pod5---bc_62	FASTQ	DNA	0.0M	0.0Mb	21	833.5	54	76	138	6932	6932	1	27.9%	7.6%	7.8	58.9%
pod5---bc_63	FASTQ	DNA	0.0M	0.0Mb	64	87.8	77	92	98	103	94	2	29.1%	1.4%	6.5	35.0%
pod5---bc_65	FASTQ	DNA	0.0M	0.0Mb	190	282.0	197	284	367	370	364	2	49.2%	17.9%	9.6	39.2%
pod5---bc_66	FASTQ	DNA	0.0M	0.0Mb	352	352.0	352	352	352	352	352	1	77.3%	35.2%	15.8	43.8%
pod5---bc_68	FASTQ	DNA	0.0M	0.0Mb	36	168.0	96	181	240	274	206	2	47.2%	20.5%	10.4	28.6%
pod5---bc_69	FASTQ	DNA	0.0M	0.0Mb	74	74.0	74	74	74	74	74	1	0.0%	0.0%	5.5	47.3%
pod5---bc_71	FASTQ	DNA	0.0M	0.0Mb	95	134.5	95	134	174	174	174	1	62.8%	0.4%	11.3	37.9%
pod5---bc_72	FASTQ	DNA	0.0M	0.0Mb	102	718.3	163	224	1026	1829	1829	1	77.0%	29.0%	14.6	41.7%
pod5---bc_73	FASTQ	DNA	0.0M	0.0Mb	60	60.0	60	60	60	60	60	1	35.0%	0.0%	13.1	18.3%
pod5---bc_74	FASTQ	DNA	0.0M	0.0Mb	399	399.0	399	399	399	399	399	1	59.1%	16.0%	12.4	40.9%
pod5---bc_75	FASTQ	DNA	0.0M	0.0Mb	103	358.1	114	144	637	1123	680	2	61.6%	20.0%	12.2	44.4%
pod5---bc_76	FASTQ	DNA	0.0M	0.0Mb	75	276.0	103	153	200	1213	760	2	76.5%	43.9%	13.4	42.6%
pod5---bc_77	FASTQ	DNA	0.0M	0.0Mb	92	627.0	100	109	894	1680	1680	1	64.2%	36.0%	11.8	42.3%
pod5---bc_78	FASTQ	DNA	0.0M	0.0Mb	41	144.8	44	110	192	373	192	2	35.4%	4.4%	6.4	34.8%
pod5---bc_79	FASTQ	DNA	0.0M	0.0Mb	91	209.7	162	177	248	438	246	4	66.8%	27.0%	12.2	33.0%
pod5---bc_80	FASTQ	DNA	0.0M	0.0Mb	72	351.3	74	197	272	1161	959	2	72.4%	28.3%	14.3	41.5%
pod5---bc_81	FASTQ	DNA	0.0M	0.0Mb	147	212.5	149	196	276	312	240	2	75.9%	29.3%	13.4	35.3%
pod5---bc_82	FASTQ	DNA	0.0M	0.0Mb	49	200.0	153	257	276	294	257	2	56.3%	9.5%	9.3	43.2%
pod5---bc_83	FASTQ	DNA	0.0M	0.0Mb	184	184.0	184	184	184	184	184	1	60.9%	15.2%	9.7	46.2%
pod5---bc_84	FASTQ	DNA	0.0M	0.0Mb	166	221.5	166	222	277	277	277	1	55.5%	17.6%	12.2	32.0%
pod5---bc_85	FASTQ	DNA	0.0M	0.0Mb	50	143.7	82	113	190	268	268	1	53.8%	14.6%	10.6	35.3%
pod5---bc_86	FASTQ	DNA	0.0M	0.0Mb	50	359.8	180	239	316	1385	396	4	57.7%	17.8%	11.3	42.6%
pod5---bc_87	FASTQ	DNA	0.0M	0.0Mb	614	621.5	614	622	629	629	629	1	73.8%	45.9%	11.5	43.1%
pod5---bc_88	FASTQ	DNA	0.0M	0.0Mb	277	277.0	277	277	277	277	277	1	92.1%	47.6%	18.8	47.3%
pod5---bc_89	FASTQ	DNA	0.0M	0.0Mb	51	61.9	55	56	67	82	56	3	0.0%	0.0%	3.8	35.6%
pod5---bc_91	FASTQ	DNA	0.0M	0.0Mb	605	605.0	605	605	605	605	605	1	77.4%	55.5%	13.4	41.5%
pod5---bc_92	FASTQ	DNA	0.0M	0.0Mb	68	266.9	167	226	282	1334	282	6	56.9%	22.2%	10.0	39.6%
pod5---bc_93	FASTQ	DNA	0.0M	0.0Mb	40	171.7	56	81	122	726	726	1	49.5%	19.7%	9.7	40.4%
pod5---bc_94	FASTQ	DNA	0.0M	0.0Mb	54	63.0	54	63	72	72	72	1	0.0%	0.0%	5.6	49.2%
pod5---bc_95	FASTQ	DNA	0.0M	0.0Mb	66	280.8	119	292	405	512	405	2	40.8%	15.8%	9.5	36.2%

Expand table

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

Sort	Column	Description	ID	Scale
\|\|	Format	File format (FASTA or FASTQ)	`seqkit-format`
\|\|	Type	Sequence type (DNA, RNA, Protein)	`seqkit-type`
\|\|	# Seqs	Number of sequences (millions)	`seqkit-num_seqs`	read_count
\|\|	Total Length	Total number of bases/residues (millions)	`seqkit-sum_len`	base_count
\|\|	Min Length	Minimum sequence length	`seqkit-min_len`
\|\|	Avg Length	Average sequence length	`seqkit-avg_len`
\|\|	Q1 Length	First quartile of sequence length	`seqkit-Q1`
\|\|	Median Length	Second quartile (Median) sequence length	`seqkit-Q2`
\|\|	Q3 Length	Third quartile of sequence length	`seqkit-Q3`
\|\|	Max Length	Maximum sequence length	`seqkit-max_len`
\|\|	Gaps	Total number of gaps	`seqkit-sum_gap`
\|\|	N50	N50 sequence length	`seqkit-N50`
\|\|	N50 Count	Number of sequences >= N50	`seqkit-N50_num`
\|\|	Q20%	Percentage of bases with quality score >= 20	`seqkit-Q20_pct`
\|\|	Q30%	Percentage of bases with quality score >= 30	`seqkit-Q30_pct`
\|\|	Avg Quality	Average quality score	`seqkit-AvgQual`
\|\|	GC%	GC content percentage	`seqkit-GC_pct`
\|\|	# N Bases	Total number of N bases (millions)	`seqkit-sum_n`

Sequence Counts

Number of sequences per sample.

Created with MultiQC

Software Versions

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

Group	Software	Version
CAT_FASTQ	cat	`9.5`
DORADO_BASECALL	dorado	`1.4.0`
DORADO_DOWNLOAD_MODEL	dorado	`1.4.0`
MINIMAP2_ALIGN	minimap2	`2.29-r1283`
MINIMAP2_INDEX	minimap2	`2.29-r1283`
NANOQ_STATS	nanoq	`0.10.0`
SAMTOOLS_CAT	samtools	`1.22.1`
SAMTOOLS_FASTQ	samtools	`1.22.1`
SAMTOOLS_SORT	samtools	`1.22.1`
SEQKIT_STATS	seqkit	`2.9.0`
SEQTAGGER2	seqtagger	`1.1a`
Workflow	Master of Pores	`v4.0`
	Nextflow	`25.10.4`

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