MultiQC Report

General Statistics

Showing ⁹³/₉₃ rows and ³⁴/₅₄ columns.

Sample Name	Nr. Input Reads	Length Input Reads	% GC Input Reads	% Trimmed	Nr. Processed Reads	Length Processed Reads	% GC Processed Reads	Nr. Reads Into Mapping	Nr. Mapped Reads	Nr. Mapped Reads Post-Filter	Endogenous DNA (%)	Nr. Mapped Reads Passed Post-Filter	Endogenous DNA Post (%)	% Dup. Mapped Reads	5 Prime C>T 1st base	5 Prime C>T 2nd base	3 Prime G>A 1st base	3 Prime G>A 2nd base	Mean Length Mapped Reads	Median read length	MT genome reads	MT genome coverage	MT to Nuclear Ratio	Nr. Dedup. Mapped Reads	Mean cov	Median cov	≥ 1X	≥ 2X	≥ 3X	≥ 4X	≥ 5X	% GC Dedup. Mapped Reads	% Dups Input Reads	Median Read Length	% Failed Input Reads	Reads Trimmed	% Collapsed	% Discarded	% Dups Processed Reads	Median Read Length	%Failed Processed Reads	% Reads Mapped	% Reads Mapped	Read length std. dev.	Genome coverage	Genome reads	% Aligned	Nr. Dedup. Total Reads	Error rate	Nr. Overall Variants	Nr. SNPs	Nr. InDels	Ts/Tv	MNP
L0_2_EG5_S82								319,373	196,782	196,782	61.62	196,782	61.62	91.4%	43.7%	28.2%	44.9%	28.1%	54.36bp	49.00bp	16,981	55.0 X	NF	16,981	55.0X	55.0X	100.0%	100.0%	100.0%	99.9%	99.9%	45%										61.6%	100.0%	20.02bp	nan X	0	100.0%	16,981	1.83%	124	124	0	23.80	0
L0_2_EG5_S82_R1_001	327,077	76 bp	51%	95.6%	319,373	57 bp	52%																										66.6%	76 bp	27%	625,366	86.8%	7.8%	68.0%	52 bp	27%
L0_2_EG5_S82_R2_001	327,077	76 bp	51%																														65.5%	76 bp	45%
L0_8_SH2_S88								72,427	40,246	40,246	55.57	40,246	55.57	78.2%	36.2%	17.7%	36.4%	19.4%	51.19bp	44.00bp	8,782	26.6 X	NF	8,782	26.6X	27.0X	100.0%	99.9%	99.9%	99.8%	99.7%	45%										55.6%	100.0%	20.53bp	nan X	0	100.0%	8,782	1.58%	98	98	0	9.89	0
L0_8_SH2_S88_R1_001	72,217	76 bp	50%	89.9%	72,427	57 bp	53%																										43.6%	76 bp	9%	129,900	78.3%	10.7%	47.3%	52 bp	36%
L0_8_SH2_S88_R2_001	72,217	76 bp	53%																														45.1%	76 bp	36%
L10_11_SCO_1338_S63								4,402,594	1,566,302	1,566,302	35.58	1,566,302	35.58	98.0%	3.7%	3.4%	3.3%	3.8%	100.06bp	101.00bp	31,609	190.0 X	NF	31,609	189.9X	192.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										35.6%	100.0%	24.03bp	nan X	0	100.0%	31,609	0.72%	42	42	0	6.00	0
L10_11_SCO_1338_S63_R1_001	3,856,368	76 bp	54%	89.3%	4,402,594	77 bp	54%																										75.6%	76 bp	27%	6,891,328	84.2%	0.8%	75.7%	77 bp	18%
L10_11_SCO_1338_S63_R2_001	3,856,368	76 bp	54%																														75.0%	76 bp	27%
L10_13_SCO_2764_S65								1,866,965	1,299,734	1,299,734	69.62	1,299,734	69.62	97.5%	6.0%	7.0%	5.9%	6.9%	88.13bp	85.00bp	32,258	170.6 X	NF	32,258	170.6X	172.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										69.6%	100.0%	23.75bp	nan X	0	100.0%	32,258	1.01%	43	43	0	5.14	0
L10_13_SCO_2764_S65_R1_001	1,654,150	76 bp	48%	88.7%	1,866,965	71 bp	50%																										78.3%	76 bp	18%	2,936,112	84.9%	1.1%	77.4%	72 bp	27%
L10_13_SCO_2764_S65_R2_001	1,654,150	76 bp	51%																														76.2%	76 bp	45%
L2_10_MPHB2_S78								4,257,909	3,485,746	3,485,746	81.87	3,485,746	81.87	99.0%	5.6%	5.9%	5.8%	5.9%	128.80bp	133.00bp	33,252	257.4 X	NF	33,252	257.3X	259.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										81.9%	100.0%	12.76bp	nan X	0	100.0%	33,252	0.99%	60	60	0	11.00	0
L2_10_MPHB2_S78_R1_001	3,741,028	76 bp	46%	89.7%	4,257,909	79 bp	46%																										75.1%	76 bp	18%	6,712,116	83.7%	1.2%	71.1%	77 bp	18%
L2_10_MPHB2_S78_R2_001	3,741,028	76 bp	47%																														72.0%	76 bp	27%
L2_11_MPHB3_S79								1,616,148	1,097,467	1,097,467	67.91	1,097,467	67.91	97.2%	7.6%	5.9%	6.5%	5.4%	92.88bp	87.00bp	30,435	169.7 X	NF	30,435	169.7X	171.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										67.9%	100.0%	25.38bp	nan X	0	100.0%	30,435	0.91%	43	43	0	5.14	0
L2_11_MPHB3_S79_R1_001	1,446,321	76 bp	49%	87.9%	1,616,148	74 bp	48%																										67.4%	76 bp	27%	2,541,826	78.2%	5.0%	66.2%	77 bp	18%
L2_11_MPHB3_S79_R2_001	1,446,321	76 bp	49%																														66.4%	76 bp	27%
L2_12_MPHB4_S80								1,504,544	716,928	716,928	47.65	716,928	47.65	97.6%	5.6%	2.5%	6.1%	3.3%	73.82bp	75.00bp	17,122	75.7 X	NF	17,122	75.7X	76.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										47.6%	100.0%	24.36bp	nan X	0	100.0%	17,122	1.14%	57	57	0	8.50	0
L2_12_MPHB4_S80_R1_001	1,293,379	76 bp	50%	84.3%	1,504,544	71 bp	55%																										78.6%	76 bp	27%	2,179,526	80.3%	1.7%	76.4%	72 bp	27%
L2_12_MPHB4_S80_R2_001	1,293,379	76 bp	55%																														76.7%	76 bp	45%
L2_1_EG1_S71								655,275	129,725	129,725	19.80	129,725	19.80	95.1%	37.9%	25.5%	37.8%	25.5%	54.03bp	48.00bp	6,385	20.3 X	NF	6,385	20.3X	20.0X	99.9%	99.9%	99.8%	99.8%	99.8%	44%										19.8%	100.0%	21.66bp	nan X	0	100.0%	6,385	2.16%	223	223	0	43.60	0
L2_1_EG1_S71_R1_001	726,506	76 bp	57%	96.2%	655,275	60 bp	58%																										65.2%	76 bp	18%	1,397,674	80.4%	14.7%	68.3%	57 bp	27%
L2_1_EG1_S71_R2_001	726,506	76 bp	56%																														62.1%	76 bp	27%
L2_2_EG2_S72								303,950	20,145	20,145	6.63	20,145	6.63	84.0%	42.1%	30.5%	44.6%	24.2%	52.23bp	45.00bp	3,214	9.8 X	NF	3,214	9.8X	9.0X	99.8%	99.4%	98.5%	96.2%	91.5%	44%										6.6%	100.0%	21.17bp	nan X	0	100.0%	3,214	2.24%	167	167	0	40.75	0
L2_2_EG2_S72_R1_001	309,416	76 bp	59%	94.4%	303,950	65 bp	62%																										47.7%	76 bp	9%	584,190	83.3%	9.2%	48.3%	62 bp	9%
L2_2_EG2_S72_R2_001	309,416	76 bp	60%																														47.1%	76 bp	9%
L2_3_EG3_S73								772,831	385,855	385,855	49.93	385,855	49.93	95.9%	41.6%	26.6%	40.0%	27.6%	57.17bp	51.00bp	15,782	53.8 X	NF	15,782	53.7X	54.0X	100.0%	100.0%	100.0%	99.9%	99.9%	44%										49.9%	100.0%	22.25bp	nan X	0	100.0%	15,782	2.37%	302	302	0	42.14	0
L2_3_EG3_S73_R1_001	816,287	76 bp	52%	97.1%	772,831	59 bp	52%																										64.0%	76 bp	18%	1,584,452	87.2%	9.1%	67.1%	52 bp	27%
L2_3_EG3_S73_R2_001	816,287	76 bp	52%																														63.0%	76 bp	36%
L4_11_MD2_S21								1,133,082	634,975	634,975	56.04	634,975	56.04	95.1%	32.5%	23.5%	29.6%	21.8%	85.28bp	83.00bp	31,295	160.1 X	NF	31,295	160.1X	162.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										56.0%	100.0%	26.55bp	nan X	0	100.0%	31,295	1.81%	83	83	0	7.30	0
L4_11_MD2_S21_R1_001	1,161,830	76 bp	51%	96.9%	1,133,082	63 bp	50%																										54.6%	76 bp	27%	2,252,120	89.1%	6.7%	55.6%	57 bp	27%
L4_11_MD2_S21_R2_001	1,161,830	76 bp	51%																														54.7%	76 bp	36%
L4_13_MB5_S23								1,866,210	1,346,962	1,346,962	72.18	1,346,962	72.18	97.5%	21.4%	18.1%	22.1%	18.1%	95.12bp	94.00bp	33,114	189.1 X	NF	33,114	189.1X	191.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										72.2%	100.0%	23.62bp	nan X	0	100.0%	33,114	1.59%	60	60	0	5.67	0
L4_13_MB5_S23_R1_001	1,887,203	76 bp	49%	97.7%	1,866,210	58 bp	47%																										62.0%	76 bp	18%	3,685,928	92.7%	4.2%	60.9%	52 bp	27%
L4_13_MB5_S23_R2_001	1,887,203	76 bp	49%																														61.5%	76 bp	36%
L4_4_MB9_S14								2,823,736	1,234,940	1,234,940	43.73	1,234,940	43.73	97.7%	28.7%	20.7%	26.7%	19.9%	71.18bp	70.00bp	28,217	120.3 X	NF	28,217	120.3X	122.0X	100.0%	100.0%	100.0%	100.0%	99.9%	45%										43.7%	100.0%	26.12bp	nan X	0	100.0%	28,217	1.67%	58	58	0	10.60	0
L4_4_MB9_S14_R1_001	2,893,020	76 bp	53%	96.7%	2,823,736	60 bp	53%																										75.7%	76 bp	27%	5,597,874	89.1%	6.7%	78.3%	52 bp	27%
L4_4_MB9_S14_R2_001	2,893,020	76 bp	53%																														73.8%	76 bp	36%
L4_5_MD5_S15								1,422,171	527,411	527,411	37.08	527,411	37.08	95.1%	27.2%	19.7%	26.4%	20.2%	80.82bp	76.00bp	26,070	126.4 X	NF	26,070	126.3X	128.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										37.1%	100.0%	27.49bp	nan X	0	100.0%	26,070	1.56%	76	76	0	14.20	0
L4_5_MD5_S15_R1_001	1,459,389	76 bp	53%	96.7%	1,422,171	63 bp	54%																										72.4%	76 bp	18%	2,823,602	88.6%	7.0%	74.5%	57 bp	27%
L4_5_MD5_S15_R2_001	1,459,389	76 bp	54%																														71.8%	76 bp	36%
L4_8_MB4_S18								2,627,582	1,479,353	1,479,353	56.30	1,479,353	56.30	97.8%	19.1%	12.8%	17.3%	12.8%	108.14bp	112.00bp	33,004	214.5 X	NF	33,004	214.4X	216.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										56.3%	100.0%	23.44bp	nan X	0	100.0%	33,004	1.17%	39	39	0	6.80	0
L4_8_MB4_S18_R1_001	2,520,646	76 bp	50%	93.1%	2,627,582	70 bp	49%																										55.7%	76 bp	18%	4,693,708	84.6%	5.6%	55.2%	72 bp	18%
L4_8_MB4_S18_R2_001	2,520,646	76 bp	50%																														55.1%	76 bp	27%
L4_9_MD12_S19								1,672,729	953,043	953,043	56.98	953,043	56.98	96.6%	26.1%	20.5%	26.4%	20.0%	95.08bp	95.00bp	32,845	187.5 X	NF	32,845	187.5X	190.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										57.0%	100.0%	23.82bp	nan X	0	100.0%	32,845	1.54%	46	46	0	8.20	0
L4_9_MD12_S19_R1_001	1,735,288	76 bp	50%	97.9%	1,672,729	62 bp	49%																										51.3%	76 bp	18%	3,396,400	90.9%	6.4%	50.5%	57 bp	27%
L4_9_MD12_S19_R2_001	1,735,288	76 bp	50%																														50.7%	76 bp	27%
L5_12_MD9_S37								1,720,015	941,495	941,495	54.74	941,495	54.74	96.5%	25.3%	19.5%	24.8%	18.4%	104.17bp	108.00bp	32,863	205.7 X	NF	32,863	205.6X	207.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										54.7%	100.0%	24.62bp	nan X	0	100.0%	32,863	1.50%	64	64	0	5.40	0
L5_12_MD9_S37_R1_001	1,729,303	76 bp	51%	96.4%	1,720,015	67 bp	50%																										49.7%	76 bp	9%	3,335,262	89.3%	5.6%	48.3%	62 bp	18%
L5_12_MD9_S37_R2_001	1,729,303	76 bp	50%																														49.5%	76 bp	27%
L5_13_BC11_S38								2,198,708	1,598,563	1,598,563	72.70	1,598,563	72.70	97.9%	10.5%	9.7%	9.5%	9.5%	112.64bp	117.00bp	33,129	224.3 X	NF	33,129	224.2X	228.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										72.7%	100.0%	21.06bp	nan X	0	100.0%	33,129	0.98%	43	43	0	4.38	0
L5_13_BC11_S38_R1_001	2,181,421	76 bp	48%	97.0%	2,198,708	66 bp	46%																										60.6%	76 bp	18%	4,231,758	92.3%	3.5%	56.2%	62 bp	27%
L5_13_BC11_S38_R2_001	2,181,421	76 bp	48%																														60.9%	76 bp	36%
L5_14_BC12_S39								1,014,747	662,406	662,406	65.28	662,406	65.28	95.0%	10.8%	11.7%	10.9%	10.4%	111.90bp	117.00bp	33,068	222.4 X	NF	33,068	222.3X	224.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										65.3%	100.0%	22.36bp	nan X	0	100.0%	33,068	0.98%	41	41	0	7.20	0
L5_14_BC12_S39_R1_001	961,972	76 bp	49%	93.3%	1,014,747	72 bp	48%																										45.4%	76 bp	9%	1,794,892	86.3%	4.1%	38.0%	72 bp	18%
L5_14_BC12_S39_R2_001	961,972	76 bp	49%																														45.0%	76 bp	9%
L5_15_BC13_S40								1,470,030	949,002	949,002	64.56	949,002	64.56	96.5%	10.3%	10.5%	9.3%	9.1%	100.17bp	101.00bp	32,979	198.4 X	NF	32,979	198.4X	200.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										64.6%	100.0%	23.03bp	nan X	0	100.0%	32,979	1.51%	45	45	0	6.50	0
L5_15_BC13_S40_R1_001	1,450,385	76 bp	51%	96.7%	1,470,030	66 bp	50%																										62.9%	76 bp	27%	2,804,128	91.9%	3.4%	61.7%	62 bp	27%
L5_15_BC13_S40_R2_001	1,450,385	76 bp	51%																														62.3%	76 bp	27%
L5_1_MD15_S26								1,465,355	735,287	735,287	50.18	735,287	50.18	95.6%	23.6%	19.2%	24.1%	19.5%	95.29bp	96.00bp	32,659	186.9 X	NF	32,659	186.8X	190.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										50.2%	100.0%	25.11bp	nan X	0	100.0%	32,659	1.33%	56	56	0	5.22	0
L5_1_MD15_S26_R1_001	1,551,279	76 bp	49%	97.8%	1,465,355	57 bp	50%																										39.0%	76 bp	9%	3,035,080	89.3%	8.1%	36.5%	52 bp	18%
L5_1_MD15_S26_R2_001	1,551,279	76 bp	50%																														39.1%	76 bp	36%
L5_2_MD7_S27								1,304,003	709,179	709,179	54.38	709,179	54.38	95.6%	27.5%	21.4%	25.8%	20.5%	86.11bp	84.00bp	31,278	161.6 X	NF	31,278	161.6X	164.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										54.4%	100.0%	26.98bp	nan X	0	100.0%	31,278	1.49%	48	48	0	8.60	0
L5_2_MD7_S27_R1_001	1,383,581	76 bp	52%	98.1%	1,304,003	60 bp	51%																										53.9%	76 bp	27%	2,713,464	89.1%	8.3%	55.4%	57 bp	27%
L5_2_MD7_S27_R2_001	1,383,581	76 bp	52%																														53.4%	76 bp	36%
L5_3_MD8_S28								1,234,395	712,571	712,571	57.73	712,571	57.73	95.4%	26.2%	20.8%	26.3%	20.1%	93.93bp	94.00bp	32,453	183.0 X	NF	32,453	183.0X	186.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										57.7%	100.0%	26.00bp	nan X	0	100.0%	32,453	1.50%	62	62	0	5.89	0
L5_3_MD8_S28_R1_001	1,280,233	76 bp	50%	96.6%	1,234,395	60 bp	50%																										51.0%	76 bp	18%	2,473,846	88.1%	7.7%	49.5%	57 bp	18%
L5_3_MD8_S28_R2_001	1,280,233	76 bp	51%																														50.8%	76 bp	45%
L5_4_MD4_S29								658,019	304,364	304,364	46.25	304,364	46.25	92.0%	29.7%	23.0%	30.0%	23.1%	58.96bp	54.00bp	24,271	85.5 X	NF	24,271	85.5X	87.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										46.2%	100.0%	21.04bp	nan X	0	100.0%	24,271	1.61%	78	78	0	14.60	0
L5_4_MD4_S29_R1_001	730,114	76 bp	53%	97.7%	658,019	50 bp	54%																										60.6%	76 bp	27%	1,427,054	85.3%	12.3%	63.5%	47 bp	27%
L5_4_MD4_S29_R2_001	730,114	76 bp	54%																														60.4%	76 bp	36%
L5_5_MD10_S30								2,079,949	1,318,319	1,318,319	63.38	1,318,319	63.38	97.5%	26.1%	20.6%	26.1%	20.4%	107.53bp	112.00bp	32,922	212.7 X	NF	32,922	212.7X	215.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										63.4%	100.0%	23.67bp	nan X	0	100.0%	32,922	1.54%	66	66	0	10.00	0
L5_5_MD10_S30_R1_001	2,037,194	76 bp	49%	95.8%	2,079,949	69 bp	49%																										60.5%	76 bp	18%	3,905,074	90.2%	3.8%	58.3%	67 bp	18%
L5_5_MD10_S30_R2_001	2,037,194	76 bp	50%																														59.3%	76 bp	27%
L5_6_MB8_S31								2,664,587	702,775	702,775	26.37	702,775	26.37	98.3%	31.8%	25.3%	30.5%	25.4%	61.00bp	54.00bp	11,841	43.0 X	NF	11,841	43.0X	43.0X	99.9%	99.8%	99.7%	99.7%	99.6%	45%										26.4%	100.0%	25.39bp	nan X	0	100.0%	11,841	2.14%	253	253	0	49.60	0
L5_6_MB8_S31_R1_001	2,866,330	76 bp	56%	97.6%	2,664,587	57 bp	57%																										75.7%	76 bp	27%	5,592,868	86.7%	10.2%	79.0%	52 bp	27%
L5_6_MB8_S31_R2_001	2,866,330	76 bp	56%																														74.6%	76 bp	27%
L5_7_MD3_S32								1,384,599	847,018	847,018	61.17	847,018	61.17	96.5%	28.9%	21.8%	29.5%	22.8%	71.30bp	69.00bp	29,874	127.6 X	NF	29,874	127.6X	131.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										61.2%	100.0%	21.97bp	nan X	0	100.0%	29,874	1.54%	68	68	0	7.50	0
L5_7_MD3_S32_R1_001	1,482,013	76 bp	50%	98.0%	1,384,599	51 bp	51%																										67.3%	76 bp	18%	2,903,456	89.1%	8.8%	68.5%	47 bp	27%
L5_7_MD3_S32_R2_001	1,482,013	76 bp	52%																														66.5%	76 bp	45%
L5_8_MD16_S33								1,957,768	1,558,908	1,558,908	79.63	1,558,908	79.63	97.9%	21.9%	17.7%	22.1%	17.9%	119.89bp	125.00bp	33,200	239.3 X	NF	33,200	239.2X	241.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										79.6%	100.0%	18.71bp	nan X	0	100.0%	33,200	1.25%	49	49	0	6.00	0
L5_8_MD16_S33_R1_001	1,860,749	76 bp	47%	95.4%	1,957,768	73 bp	46%																										63.9%	76 bp	18%	3,550,310	91.4%	1.7%	56.5%	72 bp	18%
L5_8_MD16_S33_R2_001	1,860,749	76 bp	47%																														63.8%	76 bp	27%
L8_15_HTMK99-XXII-0-4287_S49								2,927,810	1,942,088	1,942,088	66.33	1,942,088	66.33	98.7%	10.1%	7.8%	9.1%	7.5%	71.49bp	71.00bp	25,992	111.3 X	NF	25,992	111.3X	112.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										66.3%	100.0%	24.81bp	nan X	0	100.0%	25,992	1.38%	48	48	0	7.00	0
L8_15_HTMK99-XXII-0-4287_S49_R1_001	2,791,558	76 bp	49%	95.1%	2,927,810	66 bp	48%																										79.0%	76 bp	18%	5,311,292	91.7%	1.7%	80.0%	62 bp	27%
L8_15_HTMK99-XXII-0-4287_S49_R2_001	2,791,558	76 bp	49%																														77.7%	76 bp	36%
L9_1_26-52_S50								6,162,273	4,881,726	4,881,726	79.22	4,881,726	79.22	99.3%	4.0%	4.1%	3.9%	4.6%	122.60bp	126.00bp	33,254	245.0 X	NF	33,254	245.0X	246.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										79.2%	100.0%	15.73bp	nan X	0	100.0%	33,254	0.74%	40	40	0	7.00	0
L9_1_26-52_S50_R1_001	5,597,920	76 bp	47%	91.6%	6,162,273	73 bp	46%																										74.5%	76 bp	18%	10,260,892	86.5%	1.7%	73.1%	77 bp	18%
L9_1_26-52_S50_R2_001	5,597,920	76 bp	48%																														72.8%	76 bp	27%
L9_2_2777-17_S51								1,361,166	1,092,919	1,092,919	80.29	1,092,919	80.29	97.0%	6.1%	7.5%	7.0%	7.8%	120.37bp	125.00bp	33,206	240.2 X	NF	33,206	240.1X	242.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										80.3%	100.0%	18.10bp	nan X	0	100.0%	33,206	0.91%	46	46	0	5.57	0
L9_2_2777-17_S51_R1_001	1,202,390	76 bp	46%	90.3%	1,361,166	77 bp	46%																										66.6%	76 bp	18%	2,172,538	85.5%	0.7%	57.6%	77 bp	18%
L9_2_2777-17_S51_R2_001	1,202,390	76 bp	47%																														64.7%	76 bp	27%

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

Sort	Group	Column	Description	ID	Scale
\|\|	FastQC (pre-Trimming)	Nr. Input Reads	Total Sequences ()	`total_sequences`	read_count
\|\|	FastQC (pre-Trimming)	Length Input Reads	Average Read Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (pre-Trimming)	% GC Input Reads	Average % GC Content	`percent_gc`	None
\|\|	Adapter Removal	% Trimmed	% trimmed reads	`percent_aligned`	percent_aligned
\|\|	FastQC (post-Trimming)	Nr. Processed Reads	Total Sequences ()	`total_sequences`	read_count
\|\|	FastQC (post-Trimming)	Length Processed Reads	Average Read Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (post-Trimming)	% GC Processed Reads	Average % GC Content	`percent_gc`	None
\|\|	Samtools Flagstat (pre-samtools filter)	Nr. Reads Into Mapping	Total reads in the bam file ()	`flagstat_total`	read_count
\|\|	Samtools Flagstat (pre-samtools filter)	Nr. Mapped Reads	Reads Mapped in the bam file ()	`mapped_passed`	read_count
\|\|	Samtools Flagstat (post-samtools filter)	Nr. Mapped Reads Post-Filter	Total reads in the bam file ()	`flagstat_total`	read_count
\|\|	endorSpy	Endogenous DNA (%)	Endogenous DNA (%)	`endogenous_dna`	None
\|\|	Samtools Flagstat (post-samtools filter)	Nr. Mapped Reads Passed Post-Filter	Reads Mapped in the bam file ()	`mapped_passed`	read_count
\|\|	endorSpy	Endogenous DNA Post (%)	Endogenous DNA Post (%)	`endogenous_dna_post`	None
\|\|	Picard	% Dup. Mapped Reads	Mark Duplicates - Percent Duplication	`PERCENT_DUPLICATION`	None
\|\|	DamageProfiler	5 Prime C>T 1st base	5 Prime 1st base substitution frequency for C>T	`5 Prime1`	None
\|\|	DamageProfiler	5 Prime C>T 2nd base	5 Prime 2nd base substitution frequency for C>T	`5 Prime2`	None
\|\|	DamageProfiler	3 Prime G>A 1st base	3 Prime 1st base substitution frequency for G>A	`3 Prime1`	None
\|\|	DamageProfiler	3 Prime G>A 2nd base	3 Prime 2nd base substitution frequency for G>A	`3 Prime2`	None
\|\|	DamageProfiler	Mean Length Mapped Reads	Mean read length	`mean_readlength`	read_length
\|\|	DamageProfiler	Median read length	Median read length	`median`	read_length
\|\|	mtnucratio	MT genome reads	Reads on the mitochondrial genome ()	`mtreads`	read_count
\|\|	mtnucratio	MT genome coverage	Average coverage (X) on mitochondrial genome.	`mt_cov_avg`	None
\|\|	mtnucratio	MT to Nuclear Ratio	Mitochondrial to nuclear reads ratio (MTNUC)	`mt_nuc_ratio`	None
\|\|	QualiMap	Nr. Dedup. Mapped Reads	Number of mapped reads ()	`mapped_reads`	read_count
\|\|	QualiMap	Mean cov	Mean coverage	`mean_coverage`	None
\|\|	QualiMap	Median cov	Median coverage	`median_coverage`	None
\|\|	QualiMap	≥ 1X	Fraction of genome with at least 1X coverage	`1_x_pc`	None
\|\|	QualiMap	≥ 2X	Fraction of genome with at least 2X coverage	`2_x_pc`	None
\|\|	QualiMap	≥ 3X	Fraction of genome with at least 3X coverage	`3_x_pc`	None
\|\|	QualiMap	≥ 4X	Fraction of genome with at least 4X coverage	`4_x_pc`	None
\|\|	QualiMap	≥ 5X	Fraction of genome with at least 5X coverage	`5_x_pc`	None
\|\|	QualiMap	% GC Dedup. Mapped Reads	Mean GC content	`avg_gc`	None
\|\|	FastQC (pre-Trimming)	% Dups Input Reads	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (pre-Trimming)	Median Read Length	Median Read Length (bp)	`median_sequence_length`	None
\|\|	FastQC (pre-Trimming)	% Failed Input Reads	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	Adapter Removal	Reads Trimmed	Total trimmed reads ()	`aligned_total`	read_count
\|\|	Adapter Removal	% Collapsed	% collapsed reads	`percent_collapsed`	percent_aligned
\|\|	Adapter Removal	% Discarded	% discarded reads	`percent_discarded`	percent_discarded
\|\|	FastQC (post-Trimming)	% Dups Processed Reads	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (post-Trimming)	Median Read Length	Median Read Length (bp)	`median_sequence_length`	None
\|\|	FastQC (post-Trimming)	%Failed Processed Reads	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	Samtools Flagstat (pre-samtools filter)	% Reads Mapped	% Reads Mapped in the bam file	`mapped_passed_pct`	None
\|\|	Samtools Flagstat (post-samtools filter)	% Reads Mapped	% Reads Mapped in the bam file	`mapped_passed_pct`	None
\|\|	DamageProfiler	Read length std. dev.	Read length std. dev.	`std`	read_length
\|\|	mtnucratio	Genome coverage	Average coverage (X) on nuclear genome.	`nuc_cov_avg`	None
\|\|	mtnucratio	Genome reads	Reads on the nuclear genome ()	`nucreads`	read_count
\|\|	QualiMap	% Aligned	% mapped reads	`percentage_aligned`	None
\|\|	QualiMap	Nr. Dedup. Total Reads	Number of reads ()	`total_reads`	read_count
\|\|	QualiMap	Error rate	Alignment error rate. Total edit distance (SAM NM field) over the number of mapped bases	`general_error_rate`	None
\|\|	Bcftools Stats	Nr. Overall Variants	Variations total	`number_of_records`	None
\|\|	Bcftools Stats	Nr. SNPs	Variation SNPs	`number_of_SNPs`	None
\|\|	Bcftools Stats	Nr. InDels	Variation Insertions/Deletions	`number_of_indels`	None
\|\|	Bcftools Stats	Ts/Tv	Variant SNP transition / transversion ratio	`tstv`	None
\|\|	Bcftools Stats	MNP	Variation multinucleotide polymorphisms	`number_of_MNPs`	None

FastQC (pre-Trimming)

FastQC (pre-Trimming) is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

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.

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Sequence Quality Histograms

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.

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Per Sequence Quality Scores

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.

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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

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 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.

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Per Base N Content

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.

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Sequence Length Distribution

All samples have sequences of a single length (76bp).

Sequence Duplication Levels

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 (eg 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.

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Overrepresented sequences

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 over represented.

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 of 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.

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Adapter Content

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.

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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.

Min:

Max:

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Adapter Removal

Adapter Removal rapid adapter trimming, identification, and read merging .DOI: 10.1186/s13104-016-1900-2; 10.1186/1756-0500-5-337.

Retained and Discarded Reads

The number of input sequences that were retained, collapsed, and discarded. Be aware that the number of collapsed reads in the output FASTQ will be half of the numbers displayed in this plot, because both R1 and R2 of the collapsed sequences are counted here.

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Length Distribution

The length distribution of reads after processing adapter alignment.

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FastQC (post-Trimming)

FastQC (post-Trimming) is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

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.

loading..

Sequence Quality Histograms

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.

loading..

Per Sequence Quality Scores

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.

loading..

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

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 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.

loading..

Per Base N Content

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.

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Sequence Length Distribution

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

loading..

Sequence Duplication Levels

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 (eg 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.

loading..

Overrepresented sequences

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 over represented.

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 of 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.

loading..

Adapter Content

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.

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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.

Min:

Max:

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Samtools Flagstat (pre-samtools filter)

Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

Samtools Flagstat

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

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Samtools Flagstat (post-samtools filter)

Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

Samtools Flagstat

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

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Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

Mark Duplicates

Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
READS_UNMAPPED = UNMAPPED_READS

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Preseq

Preseq estimates the complexity of a library, showing how many additional unique reads are sequenced for increasing total read count. A shallow curve indicates complexity saturation. The dashed line shows a perfectly complex library where total reads = unique reads.DOI: 10.1038/nmeth.2375.

Complexity curve

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.

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DamageProfiler

DamageProfiler a tool to determine damage patterns on ancient DNA.DOI: 10.1093/bioinformatics/btab190.

3P misincorporation plot

3' misincorporation plot for G>A substitutions

This plot shows the frequency of G>A substitutions at the 3' read ends. Typically, one would observe high substitution percentages for ancient DNA, whereas modern DNA does not show these in higher extents.

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5P misincorporation plot

5' misincorporation plot for C>T substitutions

This plot shows the frequency of C>T substitutions at the 5' read ends. Typically, one would observe high substitution percentages for ancient DNA, whereas modern DNA does not show these in higher extents.

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Forward read length distribution

Read length distribution for forward strand (+) reads.

This plot shows the read length distribution of the forward reads in the investigated sample. Reads below lengths of 30bp are typically filtered, so the plot doesn't show these in many cases. A shifted distribution of read lengths towards smaller read lengths (e.g around 30-50bp) is also an indicator of ancient DNA.

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Reverse read length distribution

Read length distribution for reverse strand (-) reads.

This plot shows the read length distribution of the reverse reads in the investigated sample. Reads below lengths of 30bp are typically filtered, so the plot doesn't show these in many cases. A shifted distribution of read lengths towards smaller read lengths (e.g around 30-50bp) is also an indicator of ancient DNA.

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QualiMap

QualiMap is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.DOI: 10.1093/bioinformatics/btv566; 10.1093/bioinformatics/bts503.

Coverage histogram

Distribution of the number of locations in the reference genome with a given depth of coverage.

For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position (Sims et al. 2014).

Bases of a reference sequence (y-axis) are groupped by their depth of coverage (0×, 1×, …, N×) (x-axis). This plot shows the frequency of coverage depths relative to the reference sequence for each read dataset, which provides an indirect measure of the level and variation of coverage depth in the corresponding sequenced sample.

If reads are randomly distributed across the reference sequence, this plot should resemble a Poisson distribution (Lander & Waterman 1988), with a peak indicating approximate depth of coverage, and more uniform coverage depth being reflected in a narrower spread. The optimal level of coverage depth depends on the aims of the experiment, though it should at minimum be sufficiently high to adequately address the biological question; greater uniformity of coverage is generally desirable, because it increases breadth of coverage for a given depth of coverage, allowing equivalent results to be achieved at a lower sequencing depth (Sampson et al. 2011; Sims et al. 2014). However, it is difficult to achieve uniform coverage depth in practice, due to biases introduced during sample preparation (van Dijk et al. 2014), sequencing (Ross et al. 2013) and read mapping (Sims et al. 2014).

This plot may include a small peak for regions of the reference sequence with zero depth of coverage. Such regions may be absent from the given sample (due to a deletion or structural rearrangement), present in the sample but not successfully sequenced (due to bias in sequencing or preparation), or sequenced but not successfully mapped to the reference (due to the choice of mapping algorithm, the presence of repeat sequences, or mismatches caused by variants or sequencing errors). Related factors cause most datasets to contain some unmapped reads (Sims et al. 2014).

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Cumulative genome coverage

Percentage of the reference genome with at least the given depth of coverage.

For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position, while the breadth of coverage is the fraction of the reference sequence to which reads have been mapped with at least a given depth of coverage (Sims et al. 2014).

Defining coverage breadth in terms of coverage depth is useful, because sequencing experiments typically require a specific minimum depth of coverage over the region of interest (Sims et al. 2014), so the extent of the reference sequence that is amenable to analysis is constrained to lie within regions that have sufficient depth. With inadequate sequencing breadth, it can be difficult to distinguish the absence of a biological feature (such as a gene) from a lack of data (Green 2007).

For increasing coverage depths (1×, 2×, …, N×), coverage breadth is calculated as the percentage of the reference sequence that is covered by at least that number of reads, then plots coverage breadth (y-axis) against coverage depth (x-axis). This plot shows the relationship between sequencing depth and breadth for each read dataset, which can be used to gauge, for example, the likely effect of a minimum depth filter on the fraction of a genome available for analysis.

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GC content distribution

Each solid line represents the distribution of GC content of mapped reads for a given sample.

GC bias is the difference between the guanine-cytosine content (GC-content) of a set of sequencing reads and the GC-content of the DNA or RNA in the original sample. It is a well-known issue with sequencing systems, and may be introduced by PCR amplification, among other factors (Benjamini & Speed 2012; Ross et al. 2013).

QualiMap calculates the GC-content of individual mapped reads, then groups those reads by their GC-content (1%, 2%, …, 100%), and plots the frequency of mapped reads (y-axis) at each level of GC-content (x-axis). This plot shows the GC-content distribution of mapped reads for each read dataset, which should ideally resemble that of the original sample. It can be useful to display the GC-content distribution of an appropriate reference sequence for comparison, and QualiMap has an option to do this (see the Qualimap 2 documentation).

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Bcftools

Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.DOI: 10.1093/gigascience/giab008.

Variant Substitution Types

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Variant Quality

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Indel Distribution

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Variant depths

Read depth support distribution for called variants

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nf-core/eager Software Versions

are collected at run time from the software output.

nf-core/eager: v2.4.7
Nextflow: v21.10.6
FastQC: v0.11.9
MultiQC: v1.14
AdapterRemoval: v2.3.2
fastP: v0.20.1
BWA: v0.7.17-r1188
Bowtie2: v2.4.4
circulargenerator: v1.0
Samtools: v1.12
endorS.py: v0.4
DeDup: v0.12.8
Picard MarkDuplicates: v2.26.0
Qualimap: v2.2.2-dev
Preseq: v3.1.1
GATK HaplotypeCaller: v4.2.0.0
GATK UnifiedGenotyper: v3.5-0-g36282e4
freebayes: v1.3.5
sequenceTools: v1.5.2
VCF2genome: v0.91
MTNucRatioCalculator: v0.7
bedtools: v2.30.0
DamageProfiler: v0.4.9
bamUtil: v1.0.15
pmdtools: v0.50
angsd: v0.935
sexdeterrmine: v1.1.2
multivcfanalyzer: v0.85.2
malt: v0.6.1
kraken: v2.1.2
maltextract: v1.7
eigenstrat_snp_coverage: v1.0.2
mapDamage2: v2.2.1
bbduk: v38.92
bcftools: v1.12

nf-core/eager Workflow Summary

- this information is collected when the pipeline is started.

Pipeline Release: master
Run Name: soggy_lorenz
Input: /work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS/*_R{1,2}*.fastq.gz
Fasta Ref: /work/project/crucial/Sarah/Ref/NC_001960.1.fasta
Max Resources: 120 GB memory, 48 cpus, 4d time per job
Container: singularity - nfcore/eager:2.4.7
Output dir: ./results
Launch dir: /work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS
Working dir: /work/project/crucial/Sarah/7-EAGER/NC_001960.1_BIS_RESULTS/work
Script dir: /home/smaman/.nextflow/assets/nf-core/eager
User: smaman
Config Profile: standard
Config Profile Description: The Genotoul cluster profile
Config Profile Contact: support.bioinfo.genotoul@inrae.fr
Config Profile URL: https://bioinfo.genotoul.fr/
Config Files: /home/smaman/.nextflow/assets/nf-core/eager/nextflow.config, /work/project/crucial/Sarah/7-EAGER/crucial_nextflow.config

Toggle navigation v1.14

MultiQC Toolbox

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Tool Citations

About MultiQC

General Statistics

General Statistics: Columns

FastQC (pre-Trimming)

Sequence Counts Help

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Per Base N Content Help

Sequence Length Distribution

Sequence Duplication Levels Help

Overrepresented sequences Help

Adapter Content Help

Status Checks Help

Adapter Removal

Retained and Discarded Reads

Length Distribution

FastQC (post-Trimming)

Sequence Counts Help

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Per Base N Content Help

Sequence Length Distribution

Sequence Duplication Levels Help

Overrepresented sequences Help

Adapter Content Help

Status Checks Help

Samtools Flagstat (pre-samtools filter)

Samtools Flagstat

Samtools Flagstat (post-samtools filter)

Samtools Flagstat

Picard

Mark Duplicates Help

Preseq

Complexity curve

DamageProfiler

3P misincorporation plot Help

5P misincorporation plot Help

Forward read length distribution Help

Reverse read length distribution Help

QualiMap

Coverage histogram Help

Cumulative genome coverage Help

GC content distribution Help

Bcftools

Variant Substitution Types

Variant Quality

Indel Distribution

Variant depths

nf-core/eager Software Versions

nf-core/eager Workflow Summary

v1.14

Highlight Samples

Rename Samples

Show / Hide Samples

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Per Base N Content

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

Status Checks

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Per Base N Content

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

Status Checks

Mark Duplicates

3P misincorporation plot

5P misincorporation plot

Forward read length distribution

Reverse read length distribution

Coverage histogram

Cumulative genome coverage

GC content distribution