MultiQC Report

General Statistics

Showing ¹⁴⁷/₁₄₇ 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_1_EG4_S81								65,822	27,876	27,876	42.35	27,876	42.35	86.1%	34.5%	10.6%	36.4%	8.4%	50.81bp	45.00bp	3,868	11.5 X	NF	3,868	11.5X	11.0X	99.4%	98.6%	97.3%	94.5%	91.1%	46%										42.4%	100.0%	19.06bp	nan X	0	100.0%	3,868	1.14%	57	57	0	10.40	0
L0_1_EG4_S81_R1_001	64,533	76 bp	53%	86.8%	65,822	58 bp	57%																										47.5%	76 bp	18%	112,030	72.9%	12.6%	51.1%	57 bp	36%
L0_1_EG4_S81_R2_001	64,533	76 bp	56%																														49.0%	76 bp	36%
L0_3_EG6_S83								101,836	24,819	24,819	24.37	24,819	24.37	80.3%	37.7%	25.4%	36.8%	25.1%	56.10bp	49.00bp	4,893	16.1 X	NF	4,893	16.1X	16.0X	99.8%	99.8%	99.3%	98.1%	97.1%	46%										24.4%	100.0%	22.03bp	nan X	0	100.0%	4,893	1.51%	95	95	0	9.56	0
L0_3_EG6_S83_R1_001	96,128	76 bp	57%	90.1%	101,836	64 bp	59%																										55.5%	76 bp	18%	173,274	81.0%	6.6%	54.5%	62 bp	27%
L0_3_EG6_S83_R2_001	96,128	76 bp	57%																														54.7%	76 bp	27%
L10_12_SCO_2213_S64								1,178,009	537,693	537,693	45.64	537,693	45.64	95.9%	4.2%	4.1%	4.1%	4.0%	81.67bp	76.00bp	21,836	106.9 X	NF	21,836	106.9X	108.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										45.6%	100.0%	24.86bp	nan X	0	100.0%	21,836	0.84%	32	32	0	2.56	0
L10_12_SCO_2213_S64_R1_001	1,040,210	76 bp	52%	90.0%	1,178,009	78 bp	53%																										70.2%	76 bp	27%	1,872,310	85.1%	0.8%	69.4%	77 bp	27%
L10_12_SCO_2213_S64_R2_001	1,040,210	76 bp	53%																														69.3%	76 bp	36%
L10_1_BC5_S58								1,010,321	758,713	758,713	75.10	758,713	75.10	95.7%	5.3%	4.8%	5.0%	4.5%	111.15bp	115.00bp	33,004	220.3 X	NF	33,004	220.3X	223.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										75.1%	100.0%	20.65bp	nan X	0	100.0%	33,004	0.72%	6	6	0	0.20	0
L10_1_BC5_S58_R1_001	965,699	76 bp	47%	96.3%	1,010,321	71 bp	46%																										56.2%	76 bp	18%	1,859,492	94.0%	0.7%	43.2%	67 bp	9%
L10_1_BC5_S58_R2_001	965,699	76 bp	47%																														55.4%	76 bp	27%
L10_2_BC6_S59								1,201,526	952,239	952,239	79.25	952,239	79.25	96.5%	4.6%	5.3%	3.8%	4.3%	113.43bp	118.00bp	33,072	225.3 X	NF	33,072	225.3X	227.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										79.2%	100.0%	20.66bp	nan X	0	100.0%	33,072	0.64%	6	6	0	0.20	0
L10_2_BC6_S59_R1_001	1,112,441	76 bp	47%	93.9%	1,201,526	74 bp	47%																										64.9%	76 bp	18%	2,088,784	90.8%	0.6%	54.4%	72 bp	27%
L10_2_BC6_S59_R2_001	1,112,441	76 bp	48%																														64.1%	76 bp	36%
L10_3_BC7_S60								1,688,693	1,407,029	1,407,029	83.32	1,407,029	83.32	97.6%	4.1%	4.3%	4.1%	4.3%	106.35bp	109.00bp	33,074	211.2 X	NF	33,074	211.2X	213.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										83.3%	100.0%	22.10bp	nan X	0	100.0%	33,074	0.69%	7	7	0	0.40	0
L10_3_BC7_S60_R1_001	1,610,306	76 bp	47%	95.7%	1,688,693	67 bp	47%																										71.2%	76 bp	18%	3,081,866	93.0%	1.1%	65.4%	62 bp	18%
L10_3_BC7_S60_R2_001	1,610,306	76 bp	48%																														70.2%	76 bp	27%
L10_4_BC8_S61								1,400,028	1,091,012	1,091,012	77.93	1,091,012	77.93	97.0%	3.0%	4.0%	3.3%	3.7%	120.66bp	126.00bp	33,163	240.3 X	NF	33,163	240.3X	243.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										77.9%	100.0%	18.29bp	nan X	0	100.0%	33,163	0.48%	6	6	0	0.20	0
L10_4_BC8_S61_R1_001	1,242,933	76 bp	47%	90.8%	1,400,028	77 bp	46%																										63.7%	76 bp	18%	2,258,142	86.1%	0.6%	53.5%	77 bp	9%
L10_4_BC8_S61_R2_001	1,242,933	76 bp	47%																														62.9%	76 bp	18%
L10_5_BC9_S62								1,370,710	1,109,444	1,109,444	80.94	1,109,444	80.94	97.0%	8.6%	7.7%	7.9%	7.6%	102.55bp	104.00bp	32,916	202.6 X	NF	32,916	202.6X	204.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										80.9%	100.0%	22.14bp	nan X	0	100.0%	32,916	1.14%	9	9	0	0.50	0
L10_5_BC9_S62_R1_001	1,320,588	76 bp	47%	96.6%	1,370,710	68 bp	47%																										66.2%	76 bp	18%	2,551,706	94.6%	0.8%	60.2%	67 bp	18%
L10_5_BC9_S62_R2_001	1,320,588	76 bp	48%																														65.1%	76 bp	27%
L11_1_SCO_98_S66								1,305,731	759,682	759,682	58.18	759,682	58.18	96.0%	20.6%	16.0%	18.6%	16.0%	94.57bp	94.00bp	30,147	171.1 X	NF	30,147	171.1X	173.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										58.2%	100.0%	25.31bp	nan X	0	100.0%	30,147	1.41%	24	24	0	2.00	0
L11_1_SCO_98_S66_R1_001	1,207,281	76 bp	50%	93.8%	1,305,731	75 bp	50%																										58.4%	76 bp	27%	2,264,080	90.0%	0.9%	56.6%	77 bp	18%
L11_1_SCO_98_S66_R2_001	1,207,281	76 bp	50%																														56.1%	76 bp	27%
L11_2_SCO_81_S67								2,115,162	693,466	693,466	32.79	693,466	32.79	98.8%	22.1%	15.3%	22.1%	15.8%	70.19bp	67.00bp	8,423	35.2 X	NF	8,423	35.2X	35.0X	100.0%	100.0%	100.0%	99.9%	99.9%	45%										32.8%	100.0%	23.87bp	nan X	0	100.0%	8,423	1.74%	186	186	0	25.57	0
L11_2_SCO_81_S67_R1_001	1,925,043	76 bp	55%	92.2%	2,115,162	74 bp	56%																										75.2%	76 bp	27%	3,549,468	88.6%	0.8%	75.3%	77 bp	27%
L11_2_SCO_81_S67_R2_001	1,925,043	76 bp	56%																														74.4%	76 bp	27%
L11_3_SCO_114_S68								3,195,686	2,608,369	2,608,369	81.62	2,608,369	81.62	98.9%	21.1%	15.2%	20.1%	15.2%	89.28bp	86.00bp	27,747	148.6 X	NF	27,747	148.6X	150.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										81.6%	100.0%	24.65bp	nan X	0	100.0%	27,747	1.42%	28	28	0	3.00	0
L11_3_SCO_114_S68_R1_001	2,909,488	76 bp	47%	92.8%	3,195,686	77 bp	46%																										83.7%	76 bp	18%	5,401,630	89.2%	0.5%	83.3%	77 bp	18%
L11_3_SCO_114_S68_R2_001	2,909,488	76 bp	47%																														82.8%	76 bp	27%
L11_6_SCO_116_S69								816,645	498,339	498,339	61.02	498,339	61.02	99.0%	20.8%	16.2%	21.9%	16.8%	75.23bp	75.00bp	4,870	21.8 X	NF	4,870	21.8X	22.0X	99.9%	99.9%	99.9%	99.8%	99.6%	45%										61.0%	100.0%	23.98bp	nan X	0	100.0%	4,870	1.78%	246	246	0	26.33	0
L11_6_SCO_116_S69_R1_001	723,720	76 bp	50%	90.2%	816,645	78 bp	51%																										75.3%	76 bp	27%	1,305,250	85.3%	0.9%	73.9%	77 bp	27%
L11_6_SCO_116_S69_R2_001	723,720	76 bp	50%																														74.1%	76 bp	27%
L2_6_TP1_S75								2,824,890	2,180,543	2,180,543	77.19	2,180,543	77.19	98.5%	13.4%	10.0%	12.4%	10.2%	125.15bp	130.00bp	33,213	249.6 X	NF	33,213	249.6X	252.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										77.2%	100.0%	15.23bp	nan X	0	100.0%	33,213	0.90%	37	37	0	5.17	0
L2_6_TP1_S75_R1_001	2,551,845	76 bp	47%	92.4%	2,824,890	78 bp	46%																										69.3%	76 bp	18%	4,714,914	87.6%	0.9%	65.5%	77 bp	9%
L2_6_TP1_S75_R2_001	2,551,845	76 bp	47%																														67.6%	76 bp	18%
L2_7_TP2_S76								2,741,333	2,250,475	2,250,475	82.09	2,250,475	82.09	98.5%	8.9%	5.4%	8.3%	5.2%	118.38bp	124.00bp	33,200	236.0 X	NF	33,200	236.0X	238.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										82.1%	100.0%	19.42bp	nan X	0	100.0%	33,200	0.80%	45	45	0	4.62	0
L2_7_TP2_S76_R1_001	2,179,203	76 bp	47%	81.4%	2,741,333	82 bp	46%																										78.1%	76 bp	18%	3,548,414	73.4%	0.4%	75.4%	77 bp	18%
L2_7_TP2_S76_R2_001	2,179,203	76 bp	47%																														77.1%	76 bp	27%
L2_8_BC1_S77								1,743,031	1,360,195	1,360,195	78.04	1,360,195	78.04	97.6%	2.6%	2.9%	2.3%	3.0%	123.08bp	128.00bp	33,186	245.3 X	NF	33,186	245.3X	247.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										78.0%	100.0%	16.96bp	nan X	0	100.0%	33,186	0.48%	10	10	0	1.00	0
L2_8_BC1_S77_R1_001	1,479,584	76 bp	47%	87.2%	1,743,031	82 bp	46%																										69.5%	76 bp	18%	2,580,488	80.9%	0.6%	62.3%	77 bp	18%
L2_8_BC1_S77_R2_001	1,479,584	76 bp	47%																														68.3%	76 bp	27%
L3_10_MB13_S5								3,278,496	2,436,995	2,436,995	74.33	2,436,995	74.33	98.6%	19.5%	14.5%	19.0%	13.9%	111.18bp	115.00bp	33,097	221.0 X	NF	33,097	221.0X	223.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										74.3%	100.0%	21.50bp	nan X	0	100.0%	33,097	1.20%	31	31	0	2.44	0
L3_10_MB13_S5_R1_001	2,979,147	76 bp	48%	92.0%	3,278,496	75 bp	47%																										76.2%	76 bp	18%	5,480,834	87.0%	1.5%	75.6%	77 bp	18%
L3_10_MB13_S5_R2_001	2,979,147	76 bp	48%																														74.9%	76 bp	27%
L3_11_MB18_S6								2,688,523	1,221,051	1,221,051	45.42	1,221,051	45.42	97.6%	25.8%	20.7%	23.6%	18.7%	77.47bp	76.00bp	29,804	138.3 X	NF	29,804	138.3X	141.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										45.4%	100.0%	23.70bp	nan X	0	100.0%	29,804	1.53%	40	40	0	3.44	0
L3_11_MB18_S6_R1_001	2,810,563	76 bp	53%	98.4%	2,688,523	56 bp	55%																										77.0%	76 bp	27%	5,528,412	91.7%	6.3%	79.1%	52 bp	27%
L3_11_MB18_S6_R2_001	2,810,563	76 bp	53%																														76.4%	76 bp	27%
L3_12_MB6_S7								1,877,429	1,401,890	1,401,890	74.67	1,401,890	74.67	97.6%	20.2%	15.6%	18.8%	14.7%	114.12bp	119.00bp	33,125	227.0 X	NF	33,125	227.0X	229.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										74.7%	100.0%	20.60bp	nan X	0	100.0%	33,125	1.17%	18	18	0	1.57	0
L3_12_MB6_S7_R1_001	1,716,406	76 bp	48%	92.2%	1,877,429	74 bp	47%																										63.2%	76 bp	18%	3,163,634	86.7%	2.0%	59.2%	77 bp	18%
L3_12_MB6_S7_R2_001	1,716,406	76 bp	48%																														62.6%	76 bp	27%
L3_13_MB11_S8								763,532	371,171	371,171	48.61	371,171	48.61	91.7%	22.9%	16.7%	20.7%	15.7%	92.95bp	91.00bp	30,794	171.7 X	NF	30,794	171.7X	174.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										48.6%	100.0%	25.31bp	nan X	0	100.0%	30,794	1.36%	46	46	0	4.75	0
L3_13_MB11_S8_R1_001	730,958	76 bp	51%	93.9%	763,532	70 bp	51%																										39.3%	76 bp	18%	1,372,238	87.3%	4.1%	36.9%	72 bp	18%
L3_13_MB11_S8_R2_001	730,958	76 bp	51%																														39.2%	76 bp	18%
L3_14_MB10_S9								3,161,198	2,140,835	2,140,835	67.72	2,140,835	67.72	98.5%	15.7%	10.7%	15.8%	10.8%	113.09bp	117.00bp	33,179	225.3 X	NF	33,179	225.3X	227.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										67.7%	100.0%	20.08bp	nan X	0	100.0%	33,179	0.99%	33	33	0	2.67	0
L3_14_MB10_S9_R1_001	2,940,376	76 bp	49%	92.5%	3,161,198	71 bp	47%																										64.5%	76 bp	18%	5,438,258	86.3%	3.1%	62.4%	72 bp	18%
L3_14_MB10_S9_R2_001	2,940,376	76 bp	49%																														63.8%	76 bp	18%
L3_15_MB12_S10								2,851,513	1,486,061	1,486,061	52.11	1,486,061	52.11	98.3%	26.1%	20.4%	24.7%	19.0%	78.35bp	76.00bp	25,804	121.1 X	NF	25,804	121.1X	123.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										52.1%	100.0%	25.67bp	nan X	0	100.0%	25,804	1.72%	67	67	0	8.57	0
L3_15_MB12_S10_R1_001	2,737,929	76 bp	52%	94.5%	2,851,513	69 bp	52%																										77.7%	76 bp	27%	5,173,862	88.8%	3.5%	79.2%	67 bp	27%
L3_15_MB12_S10_R2_001	2,737,929	76 bp	52%																														76.3%	76 bp	27%
L3_1_MB15_S1								37,176	25,417	25,417	68.37	25,417	68.37	72.5%	29.0%	24.8%	30.6%	21.9%	56.35bp	51.00bp	6,987	23.2 X	NF	6,987	23.2X	23.0X	99.9%	99.6%	99.3%	98.7%	98.3%	46%										68.4%	100.0%	21.39bp	nan X	0	100.0%	6,987	1.88%	197	197	0	10.59	0
L3_1_MB15_S1_R1_001	39,644	76 bp	50%	98.2%	37,176	53 bp	49%																										54.4%	76 bp	18%	77,834	89.4%	8.4%	55.6%	47 bp	27%
L3_1_MB15_S1_R2_001	39,644	76 bp	51%																														54.3%	76 bp	36%
L3_5_SM3_S2								2,367,705	1,727,785	1,727,785	72.97	1,727,785	72.97	98.2%	18.6%	13.4%	16.5%	13.2%	100.06bp	101.00bp	31,066	186.6 X	NF	31,066	186.6X	189.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										73.0%	100.0%	24.69bp	nan X	0	100.0%	31,066	1.13%	9	9	0	0.80	0
L3_5_SM3_S2_R1_001	2,032,783	76 bp	48%	87.6%	2,367,705	80 bp	47%																										72.9%	76 bp	18%	3,562,546	81.3%	1.1%	70.8%	77 bp	18%
L3_5_SM3_S2_R2_001	2,032,783	76 bp	48%																														72.3%	76 bp	27%
L3_6_MB3_S3								3,050,524	2,416,135	2,416,135	79.20	2,416,135	79.20	98.6%	19.1%	13.7%	17.4%	12.0%	115.97bp	121.00bp	33,201	231.2 X	NF	33,201	231.2X	232.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										79.2%	100.0%	20.17bp	nan X	0	100.0%	33,201	1.13%	31	31	0	2.44	0
L3_6_MB3_S3_R1_001	2,521,914	76 bp	46%	84.7%	3,050,524	80 bp	46%																										75.1%	76 bp	18%	4,270,138	77.5%	0.8%	72.9%	77 bp	18%
L3_6_MB3_S3_R2_001	2,521,914	76 bp	47%																														74.2%	76 bp	27%
L3_9_MB17_S4								1,630,833	864,952	864,952	53.04	864,952	53.04	96.4%	24.6%	19.1%	23.2%	18.2%	87.56bp	85.00bp	31,128	163.5 X	NF	31,128	163.5X	167.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										53.0%	100.0%	24.66bp	nan X	0	100.0%	31,128	1.45%	33	33	0	2.67	0
L3_9_MB17_S4_R1_001	1,664,745	76 bp	53%	97.9%	1,630,833	61 bp	52%																										67.2%	76 bp	27%	3,260,294	92.5%	4.8%	68.2%	57 bp	27%
L3_9_MB17_S4_R2_001	1,664,745	76 bp	53%																														64.9%	76 bp	36%
L4_10_BC14_S20								3,751,082	3,088,654	3,088,654	82.34	3,088,654	82.34	98.9%	11.4%	9.8%	11.4%	9.6%	122.04bp	125.00bp	33,248	243.7 X	NF	33,248	243.6X	245.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										82.3%	100.0%	14.71bp	nan X	0	100.0%	33,248	1.16%	12	12	0	1.40	0
L4_10_BC14_S20_R1_001	3,650,240	76 bp	47%	96.6%	3,751,082	68 bp	47%																										69.1%	76 bp	18%	7,052,602	93.2%	2.0%	63.2%	67 bp	9%
L4_10_BC14_S20_R2_001	3,650,240	76 bp	48%																														67.7%	76 bp	27%
L4_12_MD1_S22								2,224,105	519,374	519,374	23.35	519,374	23.35	93.8%	29.1%	22.0%	26.2%	19.9%	102.47bp	105.00bp	32,417	199.4 X	NF	32,417	199.4X	202.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										23.4%	100.0%	24.52bp	nan X	0	100.0%	32,417	1.35%	25	25	0	3.17	0
L4_12_MD1_S22_R1_001	2,462,146	76 bp	54%	97.3%	2,224,105	60 bp	55%																										18.4%	76 bp	9%	4,792,804	83.3%	13.2%	17.6%	52 bp	18%
L4_12_MD1_S22_R2_001	2,462,146	76 bp	55%																														18.9%	76 bp	18%
L4_14_SM2_S24								3,481,546	1,633,080	1,633,080	46.91	1,633,080	46.91	98.7%	29.8%	21.8%	29.9%	23.3%	61.29bp	55.00bp	21,833	79.9 X	NF	21,833	79.9X	82.0X	100.0%	100.0%	100.0%	100.0%	99.9%	45%										46.9%	100.0%	24.00bp	nan X	0	100.0%	21,833	1.80%	114	114	0	18.00	0
L4_14_SM2_S24_R1_001	3,631,395	76 bp	51%	97.0%	3,481,546	58 bp	53%																										79.0%	76 bp	27%	7,048,324	88.2%	8.0%	81.7%	52 bp	27%
L4_14_SM2_S24_R2_001	3,631,395	76 bp	53%																														78.1%	76 bp	36%
L4_15_BC10_S25								3,478,714	2,636,591	2,636,591	75.79	2,636,591	75.79	98.7%	6.1%	5.9%	6.2%	6.0%	116.16bp	120.00bp	33,204	231.6 X	NF	33,204	231.6X	233.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										75.8%	100.0%	19.22bp	nan X	0	100.0%	33,204	0.80%	8	8	0	0.60	0
L4_15_BC10_S25_R1_001	3,220,094	76 bp	47%	93.5%	3,478,714	76 bp	47%																										76.6%	76 bp	18%	6,019,318	88.9%	1.5%	75.1%	77 bp	18%
L4_15_BC10_S25_R2_001	3,220,094	76 bp	48%																														75.4%	76 bp	27%
L4_1_MB14_S11								899,224	409,499	409,499	45.54	409,499	45.54	93.2%	27.9%	21.8%	25.7%	22.2%	73.99bp	72.00bp	28,006	124.1 X	NF	28,006	124.1X	127.0X	99.9%	99.9%	99.9%	99.9%	99.9%	45%										45.5%	100.0%	23.63bp	nan X	0	100.0%	28,006	1.58%	41	41	0	4.86	0
L4_1_MB14_S11_R1_001	947,530	76 bp	52%	98.2%	899,224	57 bp	52%																										45.7%	76 bp	9%	1,861,618	90.6%	7.2%	47.2%	52 bp	18%
L4_1_MB14_S11_R2_001	947,530	76 bp	53%																														43.5%	76 bp	27%
L4_2_MD13_S12								2,083,421	920,621	920,621	44.19	920,621	44.19	97.9%	36.8%	26.9%	36.4%	27.9%	58.41bp	53.00bp	19,150	66.7 X	NF	19,150	66.7X	68.0X	100.0%	99.9%	99.9%	99.9%	99.9%	45%										44.2%	100.0%	20.85bp	nan X	0	100.0%	19,150	2.14%	246	246	0	23.60	0
L4_2_MD13_S12_R1_001	2,191,544	76 bp	53%	97.5%	2,083,421	57 bp	54%																										78.6%	76 bp	27%	4,272,990	88.8%	8.1%	81.8%	52 bp	27%
L4_2_MD13_S12_R2_001	2,191,544	76 bp	53%																														77.7%	76 bp	36%
L4_3_MB16_S13								1,642,945	291,754	291,754	17.76	291,754	17.76	89.2%	22.5%	17.8%	21.9%	17.3%	95.86bp	96.00bp	31,577	181.6 X	NF	31,577	181.6X	184.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										17.8%	100.0%	24.62bp	nan X	0	100.0%	31,577	1.38%	18	18	0	1.57	0
L4_3_MB16_S13_R1_001	1,720,456	76 bp	56%	97.1%	1,642,945	62 bp	56%																										14.6%	76 bp	18%	3,341,468	87.8%	8.3%	12.9%	57 bp	18%
L4_3_MB16_S13_R2_001	1,720,456	76 bp	56%																														14.0%	76 bp	27%
L4_6_MB2_S16								1,613,790	1,217,285	1,217,285	75.43	1,217,285	75.43	97.3%	17.8%	13.1%	16.7%	13.2%	122.73bp	127.00bp	33,218	244.9 X	NF	33,218	244.8X	247.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										75.4%	100.0%	16.58bp	nan X	0	100.0%	33,218	0.96%	22	22	0	2.14	0
L4_6_MB2_S16_R1_001	1,454,645	76 bp	47%	91.7%	1,613,790	77 bp	47%																										60.0%	76 bp	18%	2,667,876	86.6%	1.2%	51.2%	77 bp	27%
L4_6_MB2_S16_R2_001	1,454,645	76 bp	48%																														59.8%	76 bp	27%
L4_7_MB1_S17								2,233,255	1,712,407	1,712,407	76.68	1,712,407	76.68	98.1%	17.5%	12.4%	16.0%	11.9%	124.07bp	130.00bp	33,195	247.4 X	NF	33,195	247.4X	250.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										76.7%	100.0%	17.21bp	nan X	0	100.0%	33,195	0.95%	31	31	0	2.88	0
L4_7_MB1_S17_R1_001	2,021,436	76 bp	48%	91.7%	2,233,255	77 bp	47%																										66.1%	76 bp	18%	3,705,866	85.9%	1.8%	57.9%	77 bp	18%
L4_7_MB1_S17_R2_001	2,021,436	76 bp	48%																														64.4%	76 bp	27%
L5_10_MD11_S35								1,411,309	363,019	363,019	25.72	363,019	25.72	93.4%	32.1%	22.8%	30.3%	22.1%	75.59bp	75.00bp	23,915	108.3 X	NF	23,915	108.3X	111.0X	100.0%	99.9%	99.9%	99.9%	99.9%	45%										25.7%	100.0%	25.80bp	nan X	0	100.0%	23,915	1.56%	72	72	0	7.00	0
L5_10_MD11_S35_R1_001	1,446,764	76 bp	56%	97.1%	1,411,309	62 bp	57%																										68.7%	76 bp	27%	2,810,118	89.8%	6.3%	70.6%	57 bp	27%
L5_10_MD11_S35_R2_001	1,446,764	76 bp	56%																														68.1%	76 bp	27%
L5_11_MD14_S36								2,247,403	800,055	800,055	35.60	800,055	35.60	97.0%	35.9%	28.3%	37.5%	27.8%	69.44bp	67.00bp	24,347	101.2 X	NF	24,347	101.2X	103.0X	100.0%	100.0%	100.0%	100.0%	99.9%	45%										35.6%	100.0%	24.15bp	nan X	0	100.0%	24,347	1.99%	136	136	0	18.43	0
L5_11_MD14_S36_R1_001	2,316,031	76 bp	54%	97.3%	2,247,403	61 bp	56%																										70.6%	76 bp	18%	4,504,954	89.7%	6.6%	73.1%	57 bp	27%
L5_11_MD14_S36_R2_001	2,316,031	76 bp	55%																														69.6%	76 bp	27%
L5_9_MD6_S34								1,552,461	219,625	219,625	14.15	219,625	14.15	86.5%	27.9%	20.4%	25.1%	19.7%	90.58bp	89.00bp	29,555	160.6 X	NF	29,555	160.6X	163.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										14.2%	100.0%	25.46bp	nan X	0	100.0%	29,555	1.48%	43	43	0	3.78	0
L5_9_MD6_S34_R1_001	1,709,417	76 bp	55%	97.8%	1,552,461	58 bp	57%																										12.3%	76 bp	9%	3,343,364	85.2%	12.0%	11.7%	52 bp	9%
L5_9_MD6_S34_R2_001	1,709,417	76 bp	56%																														12.9%	76 bp	18%
L6_11_SH2000-99-394-g_S46								3,294,039	2,380,631	2,380,631	72.27	2,380,631	72.27	98.7%	21.0%	18.5%	19.9%	18.4%	92.28bp	91.00bp	32,087	177.6 X	NF	32,087	177.6X	179.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										72.3%	100.0%	24.83bp	nan X	0	100.0%	32,087	1.72%	34	34	0	3.25	0
L6_11_SH2000-99-394-g_S46_R1_001	3,134,386	76 bp	47%	94.8%	3,294,039	69 bp	46%																										74.4%	76 bp	18%	5,940,118	90.4%	2.3%	73.4%	67 bp	18%
L6_11_SH2000-99-394-g_S46_R2_001	3,134,386	76 bp	48%																														65.4%	76 bp	36%
L6_13_SH2000-99-394-f_S47								1,930,918	1,348,904	1,348,904	69.86	1,348,904	69.86	97.9%	25.1%	21.8%	25.0%	21.6%	74.33bp	73.00bp	28,061	124.9 X	NF	28,061	124.9X	127.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										69.9%	100.0%	24.80bp	nan X	0	100.0%	28,061	2.21%	142	142	0	19.29	0
L6_13_SH2000-99-394-f_S47_R1_001	1,889,150	76 bp	47%	95.6%	1,930,918	64 bp	47%																										72.7%	76 bp	18%	3,613,604	90.6%	3.6%	74.5%	62 bp	18%
L6_13_SH2000-99-394-f_S47_R2_001	1,889,150	76 bp	48%																														72.5%	76 bp	36%
L6_3_SH1979-4-6843-e_S41								3,413,087	2,364,043	2,364,043	69.26	2,364,043	69.26	98.6%	8.0%	8.0%	8.0%	7.6%	98.70bp	101.00bp	32,159	190.5 X	NF	32,159	190.5X	192.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										69.3%	100.0%	25.81bp	nan X	0	100.0%	32,159	1.09%	45	45	0	5.43	0
L6_3_SH1979-4-6843-e_S41_R1_001	3,205,215	76 bp	48%	94.2%	3,413,087	73 bp	49%																										74.9%	76 bp	18%	6,037,060	89.6%	1.9%	74.8%	72 bp	18%
L6_3_SH1979-4-6843-e_S41_R2_001	3,205,215	76 bp	49%																														73.8%	76 bp	27%
L6_4_SH1979-4-6843-c_S42								3,135,458	1,704,558	1,704,558	54.36	1,704,558	54.36	98.2%	8.3%	7.6%	7.6%	7.7%	83.90bp	80.00bp	30,441	153.1 X	NF	30,441	153.1X	155.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										54.4%	100.0%	26.01bp	nan X	0	100.0%	30,441	1.19%	44	44	0	5.29	0
L6_4_SH1979-4-6843-c_S42_R1_001	2,861,558	76 bp	51%	91.3%	3,135,458	71 bp	51%																										70.8%	76 bp	18%	5,225,796	85.6%	2.4%	73.1%	72 bp	18%
L6_4_SH1979-4-6843-c_S42_R2_001	2,861,558	76 bp	51%																														69.8%	76 bp	27%
L6_5_SH1979-4-6843-d_S43								2,875,980	1,553,168	1,553,168	54.00	1,553,168	54.00	97.9%	9.4%	7.7%	8.3%	7.7%	94.15bp	93.00bp	32,074	181.2 X	NF	32,074	181.2X	183.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										54.0%	100.0%	25.31bp	nan X	0	100.0%	32,074	0.97%	8	8	0	0.60	0
L6_5_SH1979-4-6843-d_S43_R1_001	2,627,164	76 bp	49%	91.3%	2,875,980	73 bp	49%																										59.6%	76 bp	18%	4,799,442	85.4%	2.6%	60.7%	77 bp	9%
L6_5_SH1979-4-6843-d_S43_R2_001	2,627,164	76 bp	50%																														59.0%	76 bp	18%
L6_6_SH2001-106_11-b_S44								2,242,844	639,670	639,670	28.52	639,670	28.52	98.8%	28.3%	25.0%	28.6%	26.5%	57.31bp	51.00bp	7,657	26.0 X	NF	7,657	25.9X	26.0X	100.0%	99.8%	99.8%	99.6%	99.4%	45%										28.5%	100.0%	22.13bp	nan X	0	100.0%	7,657	2.49%	420	420	0	34.00	0
L6_6_SH2001-106_11-b_S44_R1_001	1,946,831	76 bp	52%	86.2%	2,242,844	71 bp	54%																										74.3%	76 bp	18%	3,354,430	79.6%	2.6%	73.7%	77 bp	27%
L6_6_SH2001-106_11-b_S44_R2_001	1,946,831	76 bp	54%																														73.1%	76 bp	45%
L6_8_SH2000-99-394-e_S45								2,740,145	1,695,012	1,695,012	61.86	1,695,012	61.86	98.4%	26.2%	21.5%	25.0%	20.9%	75.33bp	75.00bp	26,343	118.8 X	NF	26,343	118.8X	120.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										61.9%	100.0%	25.68bp	nan X	0	100.0%	26,343	2.01%	125	125	0	24.00	0
L6_8_SH2000-99-394-e_S45_R1_001	2,619,438	76 bp	47%	94.2%	2,740,145	68 bp	46%																										65.9%	76 bp	18%	4,937,364	88.8%	3.3%	66.9%	67 bp	9%
L6_8_SH2000-99-394-e_S45_R2_001	2,619,438	76 bp	48%																														65.5%	76 bp	36%
L9_13_SH2000-99-390-b_S55								1,432,694	421,665	421,665	29.43	421,665	29.43	99.6%	15.9%	11.2%	16.6%	13.3%	66.24bp	67.00bp	1,763	6.8 X	NF	1,763	6.8X	6.0X	95.9%	91.3%	84.3%	75.5%	65.9%	45%										29.4%	100.0%	24.02bp	nan X	0	100.0%	1,763	1.77%	198	198	0	6.62	0
L9_13_SH2000-99-390-b_S55_R1_001	1,178,892	76 bp	51%	80.5%	1,432,694	71 bp	56%																										84.1%	76 bp	18%	1,899,072	73.2%	2.6%	83.9%	77 bp	36%
L9_13_SH2000-99-390-b_S55_R2_001	1,178,892	76 bp	57%																														82.4%	76 bp	45%
L9_14_SH1979-4-6843-a_S56								1,872,745	491,214	491,214	26.23	491,214	26.23	98.7%	27.7%	25.1%	27.0%	26.8%	59.99bp	55.00bp	6,179	21.9 X	NF	6,179	21.9X	22.0X	100.0%	99.9%	99.9%	99.7%	99.5%	45%										26.2%	100.0%	21.37bp	nan X	0	100.0%	6,179	2.60%	483	483	0	52.78	0
L9_14_SH1979-4-6843-a_S56_R1_001	1,696,275	76 bp	52%	91.2%	1,872,745	71 bp	54%																										75.9%	76 bp	27%	3,092,378	86.8%	1.4%	76.2%	72 bp	27%
L9_14_SH1979-4-6843-a_S56_R2_001	1,696,275	76 bp	54%																														75.1%	76 bp	27%
L9_15_SH2000-99-390-c_S57								2,631,542	1,055,117	1,055,117	40.10	1,055,117	40.10	96.9%	7.4%	6.7%	6.7%	7.0%	104.66bp	109.00bp	32,232	202.5 X	NF	32,232	202.5X	204.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										40.1%	100.0%	25.03bp	nan X	0	100.0%	32,232	1.02%	45	45	0	5.43	0
L9_15_SH2000-99-390-c_S57_R1_001	2,388,944	76 bp	49%	92.4%	2,631,542	76 bp	49%																										38.4%	76 bp	9%	4,413,708	87.9%	1.0%	36.1%	77 bp	0%
L9_15_SH2000-99-390-c_S57_R2_001	2,388,944	76 bp	50%																														38.4%	76 bp	9%
L9_6_SH1979-4-6843-b_S53								1,933,328	690,978	690,978	35.74	690,978	35.74	96.1%	7.7%	7.5%	7.5%	7.3%	77.74bp	76.00bp	26,753	124.6 X	NF	26,753	124.6X	127.0X	100.0%	100.0%	100.0%	100.0%	100.0%	46%										35.7%	100.0%	24.71bp	nan X	0	100.0%	26,753	1.15%	30	30	0	2.75	0
L9_6_SH1979-4-6843-b_S53_R1_001	1,804,392	76 bp	53%	94.2%	1,933,328	72 bp	54%																										69.2%	76 bp	27%	3,400,808	90.6%	1.1%	69.4%	72 bp	18%
L9_6_SH1979-4-6843-b_S53_R2_001	1,804,392	76 bp	54%																														67.1%	76 bp	27%
L9_7_SH2000-99-394-c_S54								1,484,134	1,206,876	1,206,876	81.32	1,206,876	81.32	97.3%	17.6%	15.3%	18.1%	16.5%	102.31bp	105.00bp	32,420	199.1 X	NF	32,420	199.1X	201.0X	100.0%	100.0%	100.0%	100.0%	100.0%	45%										81.3%	100.0%	25.28bp	nan X	0	100.0%	32,420	1.40%	35	35	0	3.38	0
L9_7_SH2000-99-394-c_S54_R1_001	1,388,354	76 bp	46%	94.4%	1,484,134	71 bp	46%																										69.5%	76 bp	18%	2,621,612	90.8%	1.1%	66.0%	72 bp	18%
L9_7_SH2000-99-394-c_S54_R2_001	1,388,354	76 bp	47%																														68.1%	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.

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.

loading..

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.

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.

loading..

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:

loading..

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.

loading..

Length Distribution

The length distribution of reads after processing adapter alignment.

loading..

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.

loading..

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.

loading..

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:

loading..

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.

loading..

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.

loading..

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

loading..

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.

loading..

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.

loading..

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.

loading..

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.

loading..

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.

loading..

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).

loading..

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.

loading..

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).

loading..

Bcftools

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

Variant Substitution Types

loading..

Variant Quality

loading..

Indel Distribution

loading..

Variant depths

Read depth support distribution for called variants

loading..

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: naughty_heyrovsky
Input: /work/project/crucial/Sarah/7-EAGER/NC_024032.1_BIS/*_R{1,2}*.fastq.gz
Fasta Ref: /work/project/crucial/Sarah/Ref/NC_024032.1.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_024032.1_BIS_RESULTS
Working dir: /work/project/crucial/Sarah/7-EAGER/NC_024032.1_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

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

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