MoP4-g - pipeline: MultiQC Report

General Statistics

Showing ¹³⁶/₁₃₆ 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								0.3M	83.5Mb	302bp	117422bp	5bp	285.0bp	246	13.8	14.4
Acas_rep1_native								0.2M	101.9Mb	1639bp	196401bp	6bp	447.0bp	156	10.3	10.7
Atha_rep1_ivt								0.2M	48.6Mb	319bp	40009bp	5bp	289.0bp	266	10.2	9.5
Atha_rep1_native								0.2M	63.1Mb	1100bp	43942bp	9bp	378.0bp	145	11.2	10.9
Bnat_rep1_ivt								0.1M	22.8Mb	276bp	202701bp	5bp	239.0bp	213	13.5	14.3
Bnat_rep1_native								0.1M	27.4Mb	506bp	169481bp	6bp	276.0bp	140	9.9	9.6
Cfra_rep1_ivt								0.1M	32.1Mb	319bp	87963bp	5bp	278.0bp	248	13.5	14.0
Cfra_rep1_native								0.2M	66.6Mb	659bp	253137bp	9bp	331.0bp	173	13.0	13.4
Cowc_rep1_ivt								0.1M	47.5Mb	669bp	41322bp	5bp	480.0bp	366	14.0	14.4
Cowc_rep1_native								0.3M	277.7Mb	1788bp	72623bp	13bp	922.0bp	785	14.6	14.7
Ddis_rep1_ivt								0.3M	86.0Mb	286bp	61147bp	5bp	265.0bp	218	13.9	14.6
Ddis_rep1_native								0.5M	348.6Mb	2039bp	212321bp	9bp	708.0bp	166	15.7	16.4
Gthe_rep1_ivt								0.3M	73.9Mb	300bp	311846bp	5bp	254.0bp	205	13.4	13.8
Gthe_rep1_native								0.1M	36.6Mb	781bp	146469bp	10bp	305.0bp	155	9.8	9.5
Hsap_rep1_ivt								0.3M	73.9Mb	294bp	340972bp	5bp	264.0bp	262	12.6	13.1
Hsap_rep1_native								0.2M	116.4Mb	1635bp	110674bp	8bp	567.0bp	189	11.2	11.6
Itha_rep1_ivt								0.1M	31.1Mb	387bp	187090bp	11bp	292.0bp	200	10.0	9.6
Itha_rep1_native								0.1M	41.6Mb	808bp	46654bp	6bp	320.0bp	150	10.3	9.8
Mlei_rep1_ivt								0.2M	82.1Mb	404bp	91305bp	5bp	376.0bp	322	11.4	11.4
Mlei_rep1_native								0.2M	122.1Mb	1844bp	304001bp	8bp	543.0bp	188	10.8	11.0
Mmus_rep1_ivt								0.3M	74.9Mb	283bp	167855bp	5bp	243.0bp	240	12.7	13.1
Mmus_rep1_native								0.3M	169.2Mb	1540bp	61095bp	5bp	669.0bp	244	12.2	12.6
Mpol_rep1_ivt								0.2M	57.0Mb	364bp	351654bp	5bp	308.0bp	259	13.1	13.5
Mpol_rep1_native								0.1M	80.1Mb	1562bp	156635bp	11bp	592.0bp	182	11.4	11.8
Ngru_rep1_ivt								0.3M	128.5Mb	544bp	178589bp	5bp	410.0bp	309	13.6	14.2
Ngru_rep1_native								0.4M	230.6Mb	1355bp	54592bp	5bp	536.0bp	169	12.9	13.4
Nvec_rep1_ivt								0.1M	19.3Mb	282bp	124933bp	5bp	234.0bp	227	12.5	13.1
Nvec_rep1_native								0.3M	87.7Mb	591bp	116141bp	6bp	258.0bp	124	10.3	10.5
Scer_rep1_ivt								0.2M	50.9Mb	236bp	108375bp	5bp	226.0bp	204	13.8	14.4
Scer_rep1_native								0.3M	53.0Mb	326bp	29197bp	5bp	209.0bp	97	10.4	9.4
Scin_rep1_ivt								0.1M	44.9Mb	442bp	89096bp	7bp	373.0bp	312	10.1	10.1
Scin_rep1_native								0.2M	125.4Mb	1839bp	226803bp	7bp	619.0bp	202	11.0	11.5
Skew_rep1_ivt								0.2M	53.5Mb	350bp	180146bp	5bp	305.0bp	274	12.4	12.6
Skew_rep1_native								0.1M	29.9Mb	725bp	231195bp	13bp	384.0bp	191	11.7	11.8
Smic_rep1_ivt								0.2M	61.9Mb	403bp	212765bp	5bp	333.0bp	286	12.4	12.6
Smic_rep1_native								0.1M	44.0Mb	597bp	83545bp	5bp	345.0bp	188	11.9	12.0
Spun_rep1_ivt								0.1M	34.4Mb	362bp	116058bp	5bp	294.0bp	237	11.1	11.1
Spun_rep1_native								0.1M	68.1Mb	1781bp	206518bp	8bp	617.0bp	210	12.4	13.2
Tthe_rep1_ivt								0.1M	41.9Mb	338bp	52805bp	5bp	304.0bp	281	11.0	10.8
Tthe_rep1_native								0.4M	44.9Mb	130bp	118004bp	9bp	126.0bp	89	7.7	7.4
pod5---bc_1	0.2M	101.9Mb	447.6bp	48.9%	13.8%	10.7	1639bp
pod5---bc_2	0.2M	63.1Mb	378.2bp	48.6%	35.0%	11.8	1100bp
pod5---bc_3	0.1M	27.4Mb	276.9bp	40.4%	17.3%	9.6	506bp
pod5---bc_4	0.3M	277.7Mb	922.6bp	46.4%	30.7%	13.6	1788bp
pod5---bc_5	0.2M	66.6Mb	331.3bp	41.5%	26.7%	13.3	659bp
pod5---bc_6	0.5M	348.6Mb	708.2bp	42.0%	32.6%	14.4	2039bp
pod5---bc_7	0.1M	29.9Mb	384.5bp	42.2%	19.5%	11.0	725bp
pod5---bc_8	0.1M	36.6Mb	305.3bp	43.0%	18.4%	10.3	781bp
pod5---bc_9	0.1M	80.1Mb	593.0bp	48.1%	24.2%	11.5	1562bp
pod5---bc_10	0.4M	230.6Mb	536.5bp	44.6%	22.2%	13.5	1355bp
pod5---bc_11	0.3M	87.7Mb	258.3bp	43.8%	16.4%	10.6	591bp
pod5---bc_12	0.3M	53.0Mb	209.3bp	43.1%	22.6%	11.5	326bp
pod5---bc_13	0.1M	68.1Mb	617.2bp	43.9%	26.5%	12.7	1781bp
pod5---bc_14	0.1M	44.0Mb	345.6bp	41.5%	19.4%	11.2	597bp
pod5---bc_15	0.4M	44.9Mb	126.1bp	38.3%	10.4%	7.6	130bp
pod5---bc_16	0.2M	122.1Mb	543.5bp	45.9%	20.9%	11.7	1844bp
pod5---bc_17	0.3M	169.2Mb	669.4bp	54.4%	18.0%	12.0	1540bp
pod5---bc_18	0.2M	116.4Mb	567.3bp	55.1%	17.1%	11.0	1635bp
pod5---bc_19	0.1M	41.6Mb	320.8bp	46.3%	26.6%	10.7	808bp
pod5---bc_20	0.2M	125.4Mb	619.7bp	44.8%	27.1%	12.0	1839bp
pod5---bc_21	0.3M	83.5Mb	285.3bp	41.5%	22.1%	12.6	302bp
pod5---bc_22	0.2M	48.6Mb	289.6bp	39.6%	29.1%	9.7	319bp
pod5---bc_23	0.1M	22.8Mb	239.1bp	36.2%	22.2%	11.7	276bp
pod5---bc_24	0.1M	47.5Mb	481.0bp	40.0%	38.9%	13.2	669bp
pod5---bc_25	0.1M	32.1Mb	279.0bp	37.2%	31.0%	12.3	319bp
pod5---bc_26	0.3M	86.0Mb	265.4bp	34.4%	24.8%	13.0	286bp
pod5---bc_27	0.2M	53.5Mb	305.6bp	36.3%	33.1%	11.6	350bp
pod5---bc_28	0.3M	73.9Mb	254.0bp	36.8%	27.2%	11.7	300bp
pod5---bc_29	0.2M	57.0Mb	308.1bp	38.9%	30.0%	12.0	364bp
pod5---bc_30	0.3M	128.5Mb	410.1bp	38.4%	30.9%	12.9	544bp
pod5---bc_31	0.1M	19.3Mb	235.0bp	35.7%	21.0%	11.5	282bp
pod5---bc_32	0.2M	50.9Mb	226.9bp	38.1%	22.7%	12.9	236bp
pod5---bc_33	0.1M	34.4Mb	294.3bp	35.3%	30.0%	10.6	362bp
pod5---bc_34	0.2M	61.9Mb	333.7bp	38.2%	34.9%	11.8	403bp
pod5---bc_35	0.1M	41.9Mb	304.2bp	33.3%	29.6%	10.5	338bp
pod5---bc_36	0.2M	82.1Mb	376.5bp	39.0%	27.4%	11.1	404bp
pod5---bc_37	0.3M	74.9Mb	243.5bp	36.8%	21.5%	11.9	283bp
pod5---bc_38	0.3M	73.9Mb	264.5bp	38.7%	18.8%	11.6	294bp
pod5---bc_39	0.1M	31.1Mb	292.9bp	40.2%	18.6%	9.7	387bp
pod5---bc_40	0.1M	44.9Mb	373.1bp	38.2%	28.2%	10.2	442bp
pod5---bc_41	0.0M	0.0Mb	340.4bp	40.8%	22.1%	10.7	406bp
pod5---bc_42	0.0M	0.0Mb	303.2bp	41.6%	22.5%	10.3	937bp
pod5---bc_43	0.0M	0.3Mb	348.3bp	43.1%	13.4%	9.3	609bp
pod5---bc_44	0.0M	0.1Mb	525.3bp	51.3%	20.8%	11.3	1442bp
pod5---bc_45	0.0M	0.2Mb	220.5bp	42.1%	16.3%	9.2	346bp
pod5---bc_46	0.0M	0.1Mb	303.5bp	44.8%	25.4%	10.4	674bp
pod5---bc_47	0.0M	1.3Mb	217.7bp	42.7%	13.9%	8.9	314bp
pod5---bc_48	0.0M	0.4Mb	276.7bp	42.4%	20.3%	9.7	948bp
pod5---bc_49	0.0M	0.3Mb	320.7bp	42.0%	22.6%	10.7	546bp
pod5---bc_50	0.0M	0.2Mb	244.8bp	44.3%	14.4%	8.8	349bp
pod5---bc_51	0.0M	0.9Mb	358.7bp	42.5%	21.2%	11.1	489bp
pod5---bc_52	0.0M	0.1Mb	369.3bp	44.7%	22.5%	10.3	1060bp
pod5---bc_53	0.0M	0.3Mb	436.3bp	44.3%	14.7%	9.8	1170bp
pod5---bc_54	0.0M	0.1Mb	309.1bp	42.6%	20.0%	10.3	347bp
pod5---bc_55	0.0M	0.1Mb	354.6bp	43.7%	17.5%	9.7	554bp
pod5---bc_56	0.0M	0.1Mb	432.5bp	47.7%	18.1%	9.6	1253bp
pod5---bc_57	0.0M	0.3Mb	562.6bp	44.6%	24.2%	10.9	1556bp
pod5---bc_58	0.0M	0.1Mb	250.4bp	41.2%	19.9%	9.3	513bp
pod5---bc_59	0.0M	0.3Mb	376.7bp	41.3%	21.8%	11.3	819bp
pod5---bc_60	0.0M	0.2Mb	330.4bp	41.5%	18.2%	10.0	562bp
pod5---bc_61	0.0M	0.1Mb	272.2bp	41.8%	14.3%	9.4	670bp
pod5---bc_62	0.0M	0.2Mb	472.4bp	52.5%	15.1%	10.2	1415bp
pod5---bc_63	0.0M	0.1Mb	249.1bp	44.0%	19.1%	10.4	773bp
pod5---bc_64	0.0M	0.0Mb	249.1bp	38.1%	21.7%	9.7	403bp
pod5---bc_65	0.0M	0.1Mb	398.3bp	41.9%	20.2%	10.2	634bp
pod5---bc_66	0.0M	0.1Mb	399.1bp	42.0%	20.1%	10.6	852bp
pod5---bc_67	0.0M	0.0Mb	253.5bp	38.3%	19.4%	9.6	337bp
pod5---bc_68	0.0M	0.1Mb	341.6bp	44.0%	17.7%	10.6	451bp
pod5---bc_69	0.0M	0.0Mb	189.5bp	40.5%	31.1%	10.4	293bp
pod5---bc_70	0.0M	0.0Mb	290.3bp	42.8%	14.8%	9.7	377bp
pod5---bc_71	0.0M	0.0Mb	460.5bp	43.3%	22.9%	11.5	1275bp
pod5---bc_72	0.0M	0.1Mb	421.2bp	41.0%	24.9%	11.8	1665bp
pod5---bc_73	0.0M	0.2Mb	627.4bp	44.9%	26.4%	11.2	1851bp
pod5---bc_74	0.0M	0.1Mb	476.9bp	47.0%	18.6%	10.1	1070bp
pod5---bc_75	0.0M	0.2Mb	488.7bp	44.3%	23.1%	10.3	1121bp
pod5---bc_76	0.0M	0.3Mb	250.7bp	43.4%	21.3%	10.4	744bp
pod5---bc_77	0.0M	0.0Mb	180.1bp	41.0%	13.3%	8.4	285bp
pod5---bc_78	0.0M	0.1Mb	288.6bp	40.0%	20.9%	10.1	580bp
pod5---bc_79	0.0M	0.1Mb	250.4bp	37.9%	26.7%	11.4	306bp
pod5---bc_80	0.0M	0.2Mb	189.8bp	42.6%	15.9%	10.0	204bp
pod5---bc_81	0.0M	0.2Mb	395.0bp	42.6%	23.4%	10.8	726bp
pod5---bc_82	0.0M	0.1Mb	379.5bp	43.4%	19.9%	10.1	1136bp
pod5---bc_83	0.0M	0.0Mb	269.1bp	39.9%	17.6%	9.4	327bp
pod5---bc_84	0.0M	0.0Mb	311.7bp	38.6%	28.9%	10.7	381bp
pod5---bc_85	0.0M	0.1Mb	278.2bp	42.1%	17.9%	10.1	413bp
pod5---bc_86	0.0M	0.3Mb	295.1bp	39.2%	23.2%	10.9	358bp
pod5---bc_87	0.0M	0.1Mb	275.2bp	41.4%	23.3%	10.7	393bp
pod5---bc_88	0.0M	0.1Mb	281.6bp	41.4%	24.2%	10.5	377bp
pod5---bc_89	0.0M	0.1Mb	182.4bp	42.5%	16.9%	8.1	516bp
pod5---bc_90	0.0M	0.0Mb	351.2bp	43.8%	22.3%	9.9	1547bp
pod5---bc_91	0.0M	0.1Mb	546.2bp	41.1%	25.1%	10.8	2903bp
pod5---bc_92	0.0M	0.3Mb	292.3bp	38.8%	18.8%	10.1	325bp
pod5---bc_93	0.0M	0.2Mb	419.8bp	44.0%	24.6%	10.9	892bp
pod5---bc_94	0.0M	0.1Mb	222.8bp	39.8%	17.3%	8.3	345bp
pod5---bc_95	0.0M	0.1Mb	430.3bp	48.7%	18.4%	10.6	942bp
pod5---bc_96	0.0M	0.0Mb	672.0bp	45.9%	23.4%	11.8	1823bp

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	66056	22.6%	21974284	26.3%	285	117422	96.66%
Acas_rep1_native_s.cram	53089	23.3%	65846591	64.6%	447	196401	93.75%
Atha_rep1_ivt_s.cram	21853	13.0%	4931486	10.2%	289	40009	95.24%
Atha_rep1_native_s.cram	47200	28.3%	29556627	46.8%	378	43942	88.96%
Bnat_rep1_ivt_s.cram	10791	11.3%	2385383	10.5%	239	202701	87.24%
Bnat_rep1_native_s.cram	17484	17.7%	9266978	33.8%	276	169481	84.46%
Cfra_rep1_ivt_s.cram	52225	45.4%	11281982	35.1%	278	87963	92.37%
Cfra_rep1_native_s.cram	112676	56.1%	46663207	70.1%	331	253137	88.61%
Cowc_rep1_ivt_s.cram	53820	54.5%	24941563	52.5%	480	41322	93.30%
Cowc_rep1_native_s.cram	170278	56.6%	217852411	78.5%	922	72623	94.83%
Ddis_rep1_ivt_s.cram	36737	11.3%	16008640	18.6%	265	61147	96.96%
Ddis_rep1_native_s.cram	140379	28.5%	252390036	72.4%	708	212321	95.80%
Gthe_rep1_ivt_s.cram	41124	14.1%	11248565	15.2%	254	311846	81.29%
Gthe_rep1_native_s.cram	19326	16.1%	13896006	38.0%	305	146469	81.16%
Hsap_rep1_ivt_s.cram	160370	57.4%	25174776	34.0%	264	340972	97.61%
Hsap_rep1_native_s.cram	122590	59.7%	92090622	79.1%	567	110674	91.98%
Itha_rep1_ivt_s.cram	33617	31.7%	12331617	39.7%	292	187090	91.93%
Itha_rep1_native_s.cram	33559	25.9%	18210156	43.8%	320	46654	88.22%
Mlei_rep1_ivt_s.cram	84258	38.7%	26398014	32.2%	376	91305	93.13%
Mlei_rep1_native_s.cram	76325	34.0%	79804263	65.3%	543	304001	94.36%
Mmus_rep1_ivt_s.cram	116969	38.0%	18560414	24.8%	243	167855	96.94%
Mmus_rep1_native_s.cram	173146	68.5%	137662285	81.4%	669	61095	91.86%
Mpol_rep1_ivt_s.cram	48752	26.4%	13838504	24.3%	308	351654	90.72%
Mpol_rep1_native_s.cram	43339	32.1%	49745356	62.1%	592	156635	86.12%
Ngru_rep1_ivt_s.cram	186036	59.4%	69871496	54.4%	410	178589	97.41%
Ngru_rep1_native_s.cram	182890	42.5%	179205144	77.7%	536	54592	95.63%
Nvec_rep1_ivt_s.cram	20677	25.1%	3226588	16.7%	234	124933	96.91%
Nvec_rep1_native_s.cram	52507	15.5%	40976882	46.7%	258	116141	94.17%
Scer_rep1_ivt_s.cram	69978	31.2%	13090959	25.7%	226	108375	98.61%
Scer_rep1_native_s.cram	88568	35.0%	33202585	62.6%	209	29197	97.32%
Scin_rep1_ivt_s.cram	46889	38.9%	16541597	36.8%	373	89096	89.08%
Scin_rep1_native_s.cram	98424	48.6%	99537590	79.4%	619	226803	87.10%
Skew_rep1_ivt_s.cram	30066	17.2%	10069081	18.8%	305	180146	95.45%
Skew_rep1_native_s.cram	19456	25.0%	13175994	44.1%	384	231195	89.18%
Smic_rep1_ivt_s.cram	49784	26.8%	16698221	27.0%	333	212765	96.13%
Smic_rep1_native_s.cram	34434	27.1%	19764740	44.9%	345	83545	89.87%
Spun_rep1_ivt_s.cram	27414	23.5%	9147793	26.6%	294	116058	85.02%
Spun_rep1_native_s.cram	45017	40.8%	41122700	60.4%	617	206518	93.03%
Tthe_rep1_ivt_s.cram	29955	21.8%	10354341	24.7%	304	52805	97.50%
Tthe_rep1_native_s.cram	8751	2.5%	5227086	11.7%	126	118004	96.30%

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	0.3M	83.5Mb	302bp	117422bp	5bp	285.0bp	246	13.8	14.4
Acas_rep1_native	0.2M	101.9Mb	1639bp	196401bp	6bp	447.0bp	156	10.3	10.7
Atha_rep1_ivt	0.2M	48.6Mb	319bp	40009bp	5bp	289.0bp	266	10.2	9.5
Atha_rep1_native	0.2M	63.1Mb	1100bp	43942bp	9bp	378.0bp	145	11.2	10.9
Bnat_rep1_ivt	0.1M	22.8Mb	276bp	202701bp	5bp	239.0bp	213	13.5	14.3
Bnat_rep1_native	0.1M	27.4Mb	506bp	169481bp	6bp	276.0bp	140	9.9	9.6
Cfra_rep1_ivt	0.1M	32.1Mb	319bp	87963bp	5bp	278.0bp	248	13.5	14.0
Cfra_rep1_native	0.2M	66.6Mb	659bp	253137bp	9bp	331.0bp	173	13.0	13.4
Cowc_rep1_ivt	0.1M	47.5Mb	669bp	41322bp	5bp	480.0bp	366	14.0	14.4
Cowc_rep1_native	0.3M	277.7Mb	1788bp	72623bp	13bp	922.0bp	785	14.6	14.7
Ddis_rep1_ivt	0.3M	86.0Mb	286bp	61147bp	5bp	265.0bp	218	13.9	14.6
Ddis_rep1_native	0.5M	348.6Mb	2039bp	212321bp	9bp	708.0bp	166	15.7	16.4
Gthe_rep1_ivt	0.3M	73.9Mb	300bp	311846bp	5bp	254.0bp	205	13.4	13.8
Gthe_rep1_native	0.1M	36.6Mb	781bp	146469bp	10bp	305.0bp	155	9.8	9.5
Hsap_rep1_ivt	0.3M	73.9Mb	294bp	340972bp	5bp	264.0bp	262	12.6	13.1
Hsap_rep1_native	0.2M	116.4Mb	1635bp	110674bp	8bp	567.0bp	189	11.2	11.6
Itha_rep1_ivt	0.1M	31.1Mb	387bp	187090bp	11bp	292.0bp	200	10.0	9.6
Itha_rep1_native	0.1M	41.6Mb	808bp	46654bp	6bp	320.0bp	150	10.3	9.8
Mlei_rep1_ivt	0.2M	82.1Mb	404bp	91305bp	5bp	376.0bp	322	11.4	11.4
Mlei_rep1_native	0.2M	122.1Mb	1844bp	304001bp	8bp	543.0bp	188	10.8	11.0
Mmus_rep1_ivt	0.3M	74.9Mb	283bp	167855bp	5bp	243.0bp	240	12.7	13.1
Mmus_rep1_native	0.3M	169.2Mb	1540bp	61095bp	5bp	669.0bp	244	12.2	12.6
Mpol_rep1_ivt	0.2M	57.0Mb	364bp	351654bp	5bp	308.0bp	259	13.1	13.5
Mpol_rep1_native	0.1M	80.1Mb	1562bp	156635bp	11bp	592.0bp	182	11.4	11.8
Ngru_rep1_ivt	0.3M	128.5Mb	544bp	178589bp	5bp	410.0bp	309	13.6	14.2
Ngru_rep1_native	0.4M	230.6Mb	1355bp	54592bp	5bp	536.0bp	169	12.9	13.4
Nvec_rep1_ivt	0.1M	19.3Mb	282bp	124933bp	5bp	234.0bp	227	12.5	13.1
Nvec_rep1_native	0.3M	87.7Mb	591bp	116141bp	6bp	258.0bp	124	10.3	10.5
Scer_rep1_ivt	0.2M	50.9Mb	236bp	108375bp	5bp	226.0bp	204	13.8	14.4
Scer_rep1_native	0.3M	53.0Mb	326bp	29197bp	5bp	209.0bp	97	10.4	9.4
Scin_rep1_ivt	0.1M	44.9Mb	442bp	89096bp	7bp	373.0bp	312	10.1	10.1
Scin_rep1_native	0.2M	125.4Mb	1839bp	226803bp	7bp	619.0bp	202	11.0	11.5
Skew_rep1_ivt	0.2M	53.5Mb	350bp	180146bp	5bp	305.0bp	274	12.4	12.6
Skew_rep1_native	0.1M	29.9Mb	725bp	231195bp	13bp	384.0bp	191	11.7	11.8
Smic_rep1_ivt	0.2M	61.9Mb	403bp	212765bp	5bp	333.0bp	286	12.4	12.6
Smic_rep1_native	0.1M	44.0Mb	597bp	83545bp	5bp	345.0bp	188	11.9	12.0
Spun_rep1_ivt	0.1M	34.4Mb	362bp	116058bp	5bp	294.0bp	237	11.1	11.1
Spun_rep1_native	0.1M	68.1Mb	1781bp	206518bp	8bp	617.0bp	210	12.4	13.2
Tthe_rep1_ivt	0.1M	41.9Mb	338bp	52805bp	5bp	304.0bp	281	11.0	10.8
Tthe_rep1_native	0.4M	44.9Mb	130bp	118004bp	9bp	126.0bp	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,m5C_2OmeC,inosine_m6A_2OmeA,2OmeG [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 ⁹⁶/₉₆ 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	0.2M	101.9Mb	6	447.6	116	156	273	196401	1639	1516	60.1%	13.8%	10.7	48.9%
pod5---bc_2	FASTQ	DNA	0.2M	63.1Mb	9	378.2	116	145	321	43942	1100	2264	69.7%	35.0%	11.8	48.6%
pod5---bc_3	FASTQ	DNA	0.1M	27.4Mb	6	276.9	91	140	242	169481	506	1857	53.8%	17.3%	9.6	40.4%
pod5---bc_4	FASTQ	DNA	0.3M	277.7Mb	13	922.6	171	785	1782	72623	1788	1852	74.3%	30.7%	13.6	46.4%
pod5---bc_5	FASTQ	DNA	0.2M	66.6Mb	9	331.3	103	173	331	253137	659	2618	70.9%	26.7%	13.3	41.5%
pod5---bc_6	FASTQ	DNA	0.5M	348.6Mb	9	708.2	133	166	757	212321	2039	3394	77.2%	32.6%	14.4	42.0%
pod5---bc_7	FASTQ	DNA	0.1M	29.9Mb	13	384.5	135	191	376	231195	725	2159	58.5%	19.5%	11.0	42.2%
pod5---bc_8	FASTQ	DNA	0.1M	36.6Mb	10	305.3	89	155	234	146469	781	2114	56.4%	18.4%	10.3	43.0%
pod5---bc_9	FASTQ	DNA	0.1M	80.1Mb	11	593.0	137	182	839	156635	1562	2206	63.0%	24.2%	11.5	48.1%
pod5---bc_10	FASTQ	DNA	0.4M	230.6Mb	5	536.5	137	169	622	54592	1355	2631	71.9%	22.2%	13.5	44.6%
pod5---bc_11	FASTQ	DNA	0.3M	87.7Mb	6	258.3	91	124	215	116141	591	2064	58.2%	16.4%	10.6	43.8%
pod5---bc_12	FASTQ	DNA	0.3M	53.0Mb	5	209.3	80	97	162	29197	326	2966	64.9%	22.6%	11.5	43.1%
pod5---bc_13	FASTQ	DNA	0.1M	68.1Mb	8	617.2	135	210	709	206518	1781	2073	69.4%	26.5%	12.7	43.9%
pod5---bc_14	FASTQ	DNA	0.1M	44.0Mb	5	345.6	128	188	353	83545	597	2491	59.4%	19.4%	11.2	41.5%
pod5---bc_15	FASTQ	DNA	0.4M	44.9Mb	9	126.1	76	89	122	118004	130	1782	37.2%	10.4%	7.6	38.3%
pod5---bc_16	FASTQ	DNA	0.2M	122.1Mb	8	543.5	121	188	384	304001	1844	2219	64.8%	20.9%	11.7	45.9%
pod5---bc_17	FASTQ	DNA	0.3M	169.2Mb	5	669.4	165	244	900	61095	1540	3408	64.2%	18.0%	12.0	54.4%
pod5---bc_18	FASTQ	DNA	0.2M	116.4Mb	8	567.3	122	189	661	110674	1635	3400	60.9%	17.1%	11.0	55.1%
pod5---bc_19	FASTQ	DNA	0.1M	41.6Mb	6	320.8	87	150	278	46654	808	2209	61.8%	26.6%	10.7	46.3%
pod5---bc_20	FASTQ	DNA	0.2M	125.4Mb	7	619.7	94	202	832	226803	1839	2084	68.1%	27.1%	12.0	44.8%
pod5---bc_21	FASTQ	DNA	0.3M	83.5Mb	5	285.3	182	246	310	117422	302	1683	71.7%	22.1%	12.6	41.5%
pod5---bc_22	FASTQ	DNA	0.2M	48.6Mb	5	289.6	184	266	334	40009	319	1333	57.9%	29.1%	9.7	39.6%
pod5---bc_23	FASTQ	DNA	0.1M	22.8Mb	5	239.1	136	213	285	202701	276	1138	66.1%	22.2%	11.7	36.2%
pod5---bc_24	FASTQ	DNA	0.1M	47.5Mb	5	481.0	225	366	650	41322	669	1471	74.2%	38.9%	13.2	40.0%
pod5---bc_25	FASTQ	DNA	0.1M	32.1Mb	5	279.0	168	248	333	87963	319	1238	70.4%	31.0%	12.3	37.2%
pod5---bc_26	FASTQ	DNA	0.3M	86.0Mb	5	265.4	155	218	287	61147	286	2129	72.3%	24.8%	13.0	34.4%
pod5---bc_27	FASTQ	DNA	0.2M	53.5Mb	5	305.6	169	274	360	180146	350	1595	67.0%	33.1%	11.6	36.3%
pod5---bc_28	FASTQ	DNA	0.3M	73.9Mb	5	254.0	139	205	304	311846	300	1430	67.3%	27.2%	11.7	36.8%
pod5---bc_29	FASTQ	DNA	0.2M	57.0Mb	5	308.1	173	259	369	351654	364	1478	68.5%	30.0%	12.0	38.9%
pod5---bc_30	FASTQ	DNA	0.3M	128.5Mb	5	410.1	213	309	522	178589	544	2117	72.8%	30.9%	12.9	38.4%
pod5---bc_31	FASTQ	DNA	0.1M	19.3Mb	5	235.0	149	227	300	124933	282	793	64.8%	21.0%	11.5	35.7%
pod5---bc_32	FASTQ	DNA	0.2M	50.9Mb	5	226.9	164	204	257	108375	236	1602	70.4%	22.7%	12.9	38.1%
pod5---bc_33	FASTQ	DNA	0.1M	34.4Mb	5	294.3	154	237	355	116058	362	1371	62.1%	30.0%	10.6	35.3%
pod5---bc_34	FASTQ	DNA	0.2M	61.9Mb	5	333.7	169	286	398	212765	403	1705	68.5%	34.9%	11.8	38.2%
pod5---bc_35	FASTQ	DNA	0.1M	41.9Mb	5	304.2	180	281	349	52805	338	1602	64.0%	29.6%	10.5	33.3%
pod5---bc_36	FASTQ	DNA	0.2M	82.1Mb	5	376.5	241	322	420	91305	404	1907	66.5%	27.4%	11.1	39.0%
pod5---bc_37	FASTQ	DNA	0.3M	74.9Mb	5	243.5	166	240	297	167855	283	1495	65.2%	21.5%	11.9	36.8%
pod5---bc_38	FASTQ	DNA	0.3M	73.9Mb	5	264.5	181	262	310	340972	294	1413	65.6%	18.8%	11.6	38.7%
pod5---bc_39	FASTQ	DNA	0.1M	31.1Mb	11	292.9	84	200	321	187090	387	2170	54.9%	18.6%	9.7	40.2%
pod5---bc_40	FASTQ	DNA	0.1M	44.9Mb	7	373.1	205	312	440	89096	442	1634	58.9%	28.2%	10.2	38.2%
pod5---bc_41	FASTQ	DNA	0.0M	0.0Mb	24	340.4	146	258	364	2278	406	26	60.3%	22.1%	10.7	40.8%
pod5---bc_42	FASTQ	DNA	0.0M	0.0Mb	28	303.2	77	160	269	1816	937	10	58.7%	22.5%	10.3	41.6%
pod5---bc_43	FASTQ	DNA	0.0M	0.3Mb	27	348.3	106	196	326	4062	609	102	49.6%	13.4%	9.3	43.1%
pod5---bc_44	FASTQ	DNA	0.0M	0.1Mb	19	525.3	123	176	571	4509	1442	14	61.0%	20.8%	11.3	51.3%
pod5---bc_45	FASTQ	DNA	0.0M	0.2Mb	22	220.5	74	119	215	2693	346	89	48.6%	16.3%	9.2	42.1%
pod5---bc_46	FASTQ	DNA	0.0M	0.1Mb	21	303.5	76	158	284	3509	674	43	59.9%	25.4%	10.4	44.8%
pod5---bc_47	FASTQ	DNA	0.0M	1.3Mb	15	217.7	80	102	186	4706	314	462	46.6%	13.9%	8.9	42.7%
pod5---bc_48	FASTQ	DNA	0.0M	0.4Mb	10	276.7	62	80	214	12509	948	93	54.8%	20.3%	9.7	42.4%
pod5---bc_49	FASTQ	DNA	0.0M	0.3Mb	11	320.7	101	187	307	3895	546	104	58.8%	22.6%	10.7	42.0%
pod5---bc_50	FASTQ	DNA	0.0M	0.2Mb	19	244.8	80	135	246	5028	349	78	46.2%	14.4%	8.8	44.3%
pod5---bc_51	FASTQ	DNA	0.0M	0.9Mb	16	358.7	146	241	354	4243	489	320	63.4%	21.2%	11.1	42.5%
pod5---bc_52	FASTQ	DNA	0.0M	0.1Mb	18	369.3	77	154	314	4025	1060	33	56.6%	22.5%	10.3	44.7%
pod5---bc_53	FASTQ	DNA	0.0M	0.3Mb	22	436.3	117	192	378	6018	1170	67	52.1%	14.7%	9.8	44.3%
pod5---bc_54	FASTQ	DNA	0.0M	0.1Mb	29	309.1	128	239	324	2949	347	50	57.4%	20.0%	10.3	42.6%
pod5---bc_55	FASTQ	DNA	0.0M	0.1Mb	15	354.6	85	210	355	4918	554	33	52.8%	17.5%	9.7	43.7%
pod5---bc_56	FASTQ	DNA	0.0M	0.1Mb	18	432.5	91	183	379	4728	1253	38	49.9%	18.1%	9.6	47.7%
pod5---bc_57	FASTQ	DNA	0.0M	0.3Mb	16	562.6	146	231	737	3705	1556	63	60.8%	24.2%	10.9	44.6%
pod5---bc_58	FASTQ	DNA	0.0M	0.1Mb	19	250.4	81	104	214	3347	513	30	51.7%	19.9%	9.3	41.2%
pod5---bc_59	FASTQ	DNA	0.0M	0.3Mb	14	376.7	124	190	315	3685	819	75	61.3%	21.8%	11.3	41.3%
pod5---bc_60	FASTQ	DNA	0.0M	0.2Mb	17	330.4	114	198	298	3622	562	61	54.5%	18.2%	10.0	41.5%
pod5---bc_61	FASTQ	DNA	0.0M	0.1Mb	25	272.2	80	133	255	2457	670	24	50.2%	14.3%	9.4	41.8%
pod5---bc_62	FASTQ	DNA	0.0M	0.2Mb	21	472.4	114	199	438	6932	1415	49	55.5%	15.1%	10.2	52.5%
pod5---bc_63	FASTQ	DNA	0.0M	0.1Mb	13	249.1	80	110	195	3428	773	37	57.9%	19.1%	10.4	44.0%
pod5---bc_64	FASTQ	DNA	0.0M	0.0Mb	25	249.1	88	166	328	1141	403	18	53.9%	21.7%	9.7	38.1%
pod5---bc_65	FASTQ	DNA	0.0M	0.1Mb	23	398.3	146	228	344	4200	634	38	56.2%	20.2%	10.2	41.9%
pod5---bc_66	FASTQ	DNA	0.0M	0.1Mb	38	399.1	138	182	372	3462	852	17	58.4%	20.1%	10.6	42.0%
pod5---bc_67	FASTQ	DNA	0.0M	0.0Mb	51	253.5	82	176	284	1780	337	8	52.5%	19.4%	9.6	38.3%
pod5---bc_68	FASTQ	DNA	0.0M	0.1Mb	17	341.6	148	221	317	3796	451	50	55.9%	17.7%	10.6	44.0%
pod5---bc_69	FASTQ	DNA	0.0M	0.0Mb	42	189.5	72	113	262	642	293	7	60.9%	31.1%	10.4	40.5%
pod5---bc_70	FASTQ	DNA	0.0M	0.0Mb	37	290.3	100	188	240	1991	377	7	51.2%	14.8%	9.7	42.8%
pod5---bc_71	FASTQ	DNA	0.0M	0.0Mb	31	460.5	140	198	387	1928	1275	13	62.7%	22.9%	11.5	43.3%
pod5---bc_72	FASTQ	DNA	0.0M	0.1Mb	21	421.2	100	186	316	3794	1665	13	64.8%	24.9%	11.8	41.0%
pod5---bc_73	FASTQ	DNA	0.0M	0.2Mb	18	627.4	114	208	725	3612	1851	38	64.1%	26.4%	11.2	44.9%
pod5---bc_74	FASTQ	DNA	0.0M	0.1Mb	17	476.9	140	221	433	3816	1070	20	52.5%	18.6%	10.1	47.0%
pod5---bc_75	FASTQ	DNA	0.0M	0.2Mb	24	488.7	140	266	438	4182	1121	44	57.7%	23.1%	10.3	44.3%
pod5---bc_76	FASTQ	DNA	0.0M	0.3Mb	19	250.7	80	111	189	3728	744	73	59.2%	21.3%	10.4	43.4%
pod5---bc_77	FASTQ	DNA	0.0M	0.0Mb	35	180.1	64	84	166	1827	285	18	46.4%	13.3%	8.4	41.0%
pod5---bc_78	FASTQ	DNA	0.0M	0.1Mb	20	288.6	80	150	276	3276	580	35	57.8%	20.9%	10.1	40.0%
pod5---bc_79	FASTQ	DNA	0.0M	0.1Mb	17	250.4	132	186	294	3560	306	88	65.0%	26.7%	11.4	37.9%
pod5---bc_80	FASTQ	DNA	0.0M	0.2Mb	25	189.8	83	107	172	6460	204	136	55.2%	15.9%	10.0	42.6%
pod5---bc_81	FASTQ	DNA	0.0M	0.2Mb	19	395.0	143	234	386	3553	726	52	59.6%	23.4%	10.8	42.6%
pod5---bc_82	FASTQ	DNA	0.0M	0.1Mb	23	379.5	91	169	293	6015	1136	20	53.0%	19.9%	10.1	43.4%
pod5---bc_83	FASTQ	DNA	0.0M	0.0Mb	25	269.1	103	187	303	3076	327	34	48.7%	17.6%	9.4	39.9%
pod5---bc_84	FASTQ	DNA	0.0M	0.0Mb	13	311.7	151	259	365	2796	381	31	62.3%	28.9%	10.7	38.6%
pod5---bc_85	FASTQ	DNA	0.0M	0.1Mb	25	278.2	90	159	280	2276	413	24	55.3%	17.9%	10.1	42.1%
pod5---bc_86	FASTQ	DNA	0.0M	0.3Mb	15	295.1	138	219	334	2833	358	178	61.0%	23.2%	10.9	39.2%
pod5---bc_87	FASTQ	DNA	0.0M	0.1Mb	42	275.2	94	168	270	3577	393	35	60.8%	23.3%	10.7	41.4%
pod5---bc_88	FASTQ	DNA	0.0M	0.1Mb	24	281.6	102	197	312	3687	377	54	59.2%	24.2%	10.5	41.4%
pod5---bc_89	FASTQ	DNA	0.0M	0.1Mb	39	182.4	58	68	110	3670	516	22	49.5%	16.9%	8.1	42.5%
pod5---bc_90	FASTQ	DNA	0.0M	0.0Mb	47	351.2	65	86	220	3555	1547	9	56.8%	22.3%	9.9	43.8%
pod5---bc_91	FASTQ	DNA	0.0M	0.1Mb	14	546.2	111	174	313	4591	2903	11	62.7%	25.1%	10.8	41.1%
pod5---bc_92	FASTQ	DNA	0.0M	0.3Mb	25	292.3	128	218	301	4953	325	150	55.2%	18.8%	10.1	38.8%
pod5---bc_93	FASTQ	DNA	0.0M	0.2Mb	16	419.8	140	224	380	2849	892	54	60.5%	24.6%	10.9	44.0%
pod5---bc_94	FASTQ	DNA	0.0M	0.1Mb	33	222.8	70	95	256	2473	345	39	48.6%	17.3%	8.3	39.8%
pod5---bc_95	FASTQ	DNA	0.0M	0.1Mb	22	430.3	155	225	362	4304	942	32	58.3%	18.4%	10.6	48.7%
pod5---bc_96	FASTQ	DNA	0.0M	0.0Mb	32	672.0	170	248	853	3230	1823	10	64.5%	23.4%	11.8	45.9%

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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