MultiQC Report

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

This report has been generated by the nf-core/eager analysis pipeline. For information about how to interpret these results, please see the documentation.

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Report generated on 2021-12-17, 16:35 based on data in:

/home/bartholdybp/.nextflow/assets/nf-core/eager/assets/multiqc_config.yaml
/data/bartholdybp/analysis/158103/work/c8/34e052e3bd65f4888819e0fa6b4b8d

General Statistics

Showing ⁴⁶⁶/₄₆₆ rows and ¹⁶/₂₇ columns.

Sample Name	Seqs	Length	% GC	GC content	% Trimmed	Seqs	Length	% GC	% Unclassified	Reads	Reads Mapped	Reads	Endogenous DNA (%)	Reads Mapped	Endogenous DNA Post (%)	% Dups	% Dups	% Failed	% Duplication	% > Q30	Mb Q30 bases	% PF	Reads Trimmed	% Dups	% Failed	% Enterococcus faecalis	% Top 5 Species
LIB030.A0117									63.6%	3,310	418	418	12.63	418	12.63	5.0%										0.0%	0.1%
LIB030.A0117.SG1.1_S0_L001_R1_001	2,236	151 bp	66%		94.8%	819	89 bp	59%									47.1%	45%					2,974	2.6%	18%
LIB030.A0117.SG1.1_S0_L001_R2_001	2,236	151 bp	75%														50.8%	55%
LIB030.A0117.SG1.1_S0_L002_R1_001	2,127	151 bp	66%		94.4%	826	87 bp	59%									46.0%	45%					2,848	1.8%	27%
LIB030.A0117.SG1.1_S0_L002_R2_001	2,127	151 bp	75%														50.0%	45%
LIB030.A0117.SG1.1_S0_L003_R1_001	2,477	151 bp	67%		95.9%	815	84 bp	59%									43.7%	45%					3,284	1.5%	27%
LIB030.A0117.SG1.1_S0_L003_R2_001	2,477	151 bp	76%														50.8%	55%
LIB030.A0117.SG1.1_S0_L004_R1_001	2,220	151 bp	66%		95.7%	850	86 bp	59%									44.0%	45%					3,018	1.3%	18%
LIB030.A0117.SG1.1_S0_L004_R2_001	2,220	151 bp	75%														46.9%	45%
LIB030.A0117_L1_polyg				52.2%															7.5%	72.2%	0.2	70.1%
LIB030.A0117_L2_polyg				52.3%															10.5%	71.5%	0.2	70.9%
LIB030.A0117_L3_polyg				52.6%															6.6%	67.8%	0.2	69.2%
LIB030.A0117_L4_polyg				52.6%															7.2%	70.3%	0.2	71.0%
SYN001.A0101									23.1%	13,031,258	2,848,845	2,848,845	21.86	2,848,845	21.86	6.2%										0.0%	31.9%
SYN001.A0101.SG1.1_S0_L001_R1_001	3,201,011	151 bp	51%		97.7%	3,235,522	129 bp	50%									3.5%	18%					6,239,576	3.0%	18%
SYN001.A0101.SG1.1_S0_L001_R2_001	3,201,011	151 bp	50%														3.5%	18%
SYN001.A0101.SG1.1_S0_L002_R1_001	3,165,656	151 bp	51%		97.7%	3,202,714	129 bp	50%									3.5%	18%					6,166,528	3.0%	18%
SYN001.A0101.SG1.1_S0_L002_R2_001	3,165,656	151 bp	50%														3.4%	18%
SYN001.A0101.SG1.1_S0_L003_R1_001	3,296,632	151 bp	52%		97.5%	3,337,491	128 bp	50%									3.6%	27%					6,409,058	3.2%	18%
SYN001.A0101.SG1.1_S0_L003_R2_001	3,296,632	151 bp	50%														3.6%	18%
SYN001.A0101.SG1.1_S0_L004_R1_001	3,218,142	151 bp	51%		97.7%	3,255,531	129 bp	50%									3.7%	18%					6,267,282	3.3%	18%
SYN001.A0101.SG1.1_S0_L004_R2_001	3,218,142	151 bp	50%														3.6%	18%
SYN001.A0101_L1_polyg				49.2%															1.8%	78.9%	731.5	99.7%
SYN001.A0101_L2_polyg				49.3%															1.8%	79.1%	725.3	99.7%
SYN001.A0101_L3_polyg				49.7%															1.9%	76.4%	728.9	99.7%
SYN001.A0101_L4_polyg				49.5%															1.9%	78.4%	730.6	99.7%
SYN002.A0101									23.8%	14,403,299	520,369	520,369	3.61	520,369	3.61	5.4%										0.0%	25.2%
SYN002.A0101.SG1.1_S0_L001_R1_001	3,523,270	151 bp	50%		98.0%	3,588,373	142 bp	50%									3.6%	18%					6,888,478	3.2%	18%
SYN002.A0101.SG1.1_S0_L001_R2_001	3,523,270	151 bp	50%														3.4%	27%
SYN002.A0101.SG1.1_S0_L002_R1_001	3,472,935	151 bp	50%		97.9%	3,538,388	142 bp	50%									3.5%	18%					6,780,600	3.1%	18%
SYN002.A0101.SG1.1_S0_L002_R2_001	3,472,935	151 bp	50%														3.5%	27%
SYN002.A0101.SG1.1_S0_L003_R1_001	3,593,017	151 bp	50%		97.7%	3,669,030	141 bp	50%									3.6%	18%					7,002,610	3.2%	18%
SYN002.A0101.SG1.1_S0_L003_R2_001	3,593,017	151 bp	50%														3.6%	27%
SYN002.A0101.SG1.1_S0_L004_R1_001	3,539,999	151 bp	50%		97.9%	3,607,508	142 bp	50%									3.6%	18%					6,910,702	3.2%	18%
SYN002.A0101.SG1.1_S0_L004_R2_001	3,539,999	151 bp	50%														3.6%	27%
SYN002.A0101_L1_polyg				49.5%															1.6%	81.1%	843.3	99.8%
SYN002.A0101_L2_polyg				49.5%															1.6%	81.3%	832.7	99.7%
SYN002.A0101_L3_polyg				49.7%															1.6%	78.6%	832.8	99.8%
SYN002.A0101_L4_polyg				49.6%															1.6%	80.6%	842.0	99.7%
SYN003.A0101									29.2%	13,273,382	725,245	725,245	5.46	725,245	5.46	6.0%										0.0%	14.5%
SYN003.A0101.SG1.1_S0_L001_R1_001	3,264,106	151 bp	50%		98.4%	3,302,672	138 bp	50%									2.7%	18%					6,406,650	2.5%	18%
SYN003.A0101.SG1.1_S0_L001_R2_001	3,264,106	151 bp	50%														2.7%	27%
SYN003.A0101.SG1.1_S0_L002_R1_001	3,217,861	151 bp	50%		98.3%	3,257,791	139 bp	50%									2.7%	18%					6,308,162	2.4%	18%
SYN003.A0101.SG1.1_S0_L002_R2_001	3,217,861	151 bp	50%														2.7%	27%
SYN003.A0101.SG1.1_S0_L003_R1_001	3,343,453	151 bp	51%		98.1%	3,389,414	138 bp	50%									2.8%	18%					6,545,000	2.6%	18%
SYN003.A0101.SG1.1_S0_L003_R2_001	3,343,453	151 bp	50%														2.9%	27%
SYN003.A0101.SG1.1_S0_L004_R1_001	3,283,362	151 bp	50%		98.3%	3,323,505	138 bp	50%									2.8%	18%					6,434,712	2.6%	18%
SYN003.A0101.SG1.1_S0_L004_R2_001	3,283,362	151 bp	50%														2.9%	27%
SYN003.A0101_L1_polyg				49.4%															1.8%	80.0%	769.6	99.8%
SYN003.A0101_L2_polyg				49.4%															1.8%	80.2%	760.4	99.7%
SYN003.A0101_L3_polyg				49.7%															1.8%	77.6%	764.0	99.7%
SYN003.A0101_L4_polyg				49.5%															1.8%	79.5%	769.4	99.7%
SYN005.I0101									33.4%	13,144,417	4,235	4,235	0.03	4,235	0.03	86.3%										8.1%	25.9%
SYN005.I0101.SG1.1_S0_L001_R1_001	3,402,725	151 bp	44%		89.0%	3,901,121	160 bp	43%									4.4%	9%					6,049,508	4.4%	9%
SYN005.I0101.SG1.1_S0_L001_R2_001	3,402,725	151 bp	44%														4.3%	9%
SYN005.I0101.SG1.1_S0_L002_R1_001					88.8%	1,318,206	160 bp	44%															2,033,712	1.8%	9%
SYN005.I0101.SG1.1_S0_L002_R2_001	3,387,240	151 bp	44%														4.3%	9%
SYN005.I0101.SG1.1_S0_L003_R1_001	3,472,826	151 bp	44%		88.8%	3,984,965	159 bp	44%									4.5%	9%					6,159,240	4.6%	18%
SYN005.I0101.SG1.1_S0_L003_R2_001	3,472,826	151 bp	44%														4.4%	9%
SYN005.I0101.SG1.1_S0_L004_R1_001	3,438,536	151 bp	44%		89.0%	3,940,125	160 bp	44%									4.6%	9%					6,105,530	4.6%	9%
SYN005.I0101.SG1.1_S0_L004_R2_001	3,438,536	151 bp	44%														4.4%	9%
SYN005.I0101_L1_polyg				43.8%															1.1%	82.2%	835.0	99.9%
SYN005.I0101_L2_polyg				43.9%															0.9%	82.3%	281.8	99.8%
SYN005.I0101_L3_polyg				44.0%															1.1%	80.0%	829.0	99.9%
SYN005.I0101_L4_polyg				43.9%															1.1%	82.0%	840.6	99.8%
SYN006.I0101									27.1%	11,629,882	3,674	3,674	0.03	3,674	0.03	85.8%										19.5%	43.1%
SYN006.I0101.SG1.1_S0_L001_R1_001	3,414,682	151 bp	43%		90.1%	3,864,506	159 bp	42%									4.7%	18%					6,145,592	4.6%	18%
SYN006.I0101.SG1.1_S0_L001_R2_001	3,414,682	151 bp	43%														4.6%	18%
SYN006.I0101.SG1.1_S0_L002_R1_001	3,375,640	151 bp	43%		90.0%	3,824,670	159 bp	42%									4.7%	18%					6,066,110	4.6%	18%
SYN006.I0101.SG1.1_S0_L002_R2_001	3,375,640	151 bp	43%														4.5%	18%
SYN006.I0101.SG1.1_S0_L003_R1_001	3,479,062	151 bp	43%		90.0%	3,938,020	158 bp	42%									4.9%	18%					6,253,628	4.9%	18%
SYN006.I0101.SG1.1_S0_L003_R2_001	3,479,062	151 bp	43%														4.7%	18%
SYN006.I0101.SG1.1_S0_L004_R1_001	3,433,406	151 bp	43%		90.4%	2,686	158 bp	42%									4.9%	18%					4,296	0.0%	9%
SYN006.I0101_L1_polyg				42.8%															1.1%	82.4%	839.1	99.9%
SYN006.I0101_L2_polyg				42.9%															1.1%	82.6%	831.6	99.9%
SYN006.I0101_L3_polyg				43.0%															1.1%	80.3%	833.2	99.9%
SYN006.I0101_L4_polyg				43.0%															0.0%	81.2%	0.6	100.0%
SYN008.I0101									38.0%	15,319,529	7,088	7,088	0.05	7,088	0.05	82.3%										10.2%	19.1%
SYN008.I0101.SG1.1_S0_L001_R1_001	3,802,696	151 bp	45%		99.4%	3,805,473	131 bp	43%									5.5%	9%					7,547,702	4.8%	9%
SYN008.I0101.SG1.1_S0_L001_R2_001	3,802,696	151 bp	44%														5.4%	18%
SYN008.I0101.SG1.1_S0_L002_R1_001	3,770,200	151 bp	45%		99.3%	3,772,779	131 bp	43%									5.5%	9%					7,475,030	4.7%	9%
SYN008.I0101.SG1.1_S0_L002_R2_001	3,770,200	151 bp	44%														5.4%	18%
SYN008.I0101.SG1.1_S0_L003_R1_001	3,891,742	151 bp	45%		99.3%	3,897,069	130 bp	43%									5.7%	18%					7,718,552	5.0%	9%
SYN008.I0101.SG1.1_S0_L003_R2_001	3,891,742	151 bp	44%														5.7%	18%
SYN008.I0101.SG1.1_S0_L004_R1_001	3,842,106	151 bp	45%		99.4%	3,844,208	131 bp	43%									5.7%	9%					7,618,578	5.0%	9%
SYN008.I0101.SG1.1_S0_L004_R2_001	3,842,106	151 bp	44%														5.7%	18%
SYN008.I0101_L1_polyg				43.9%															1.5%	81.2%	912.0	99.9%
SYN008.I0101_L2_polyg				43.9%															1.5%	81.3%	906.0	99.8%
SYN008.I0101_L3_polyg				44.1%															1.5%	79.2%	910.7	99.8%
SYN008.I0101_L4_polyg				44.0%															1.5%	81.0%	918.9	99.8%
SYN009.I0101									48.4%	15,828,420	7,052	7,052	0.04	7,052	0.04	82.1%										11.7%	26.8%
SYN009.I0101.SG1.1_S0_L001_R1_001	3,945,861	151 bp	49%		99.5%	3,930,954	115 bp	47%									3.1%	9%					7,842,034	2.5%	9%
SYN009.I0101.SG1.1_S0_L001_R2_001	3,945,861	151 bp	48%														3.1%	18%
SYN009.I0101.SG1.1_S0_L002_R1_001	3,903,912	151 bp	49%		99.5%	3,889,903	115 bp	47%									3.1%	18%					7,755,312	2.4%	9%
SYN009.I0101.SG1.1_S0_L002_R2_001	3,903,912	151 bp	48%														3.0%	18%
SYN009.I0101.SG1.1_S0_L003_R1_001	4,052,653	151 bp	49%		99.4%	4,041,005	115 bp	47%									3.3%	18%					8,044,648	2.7%	9%
SYN009.I0101.SG1.1_S0_L003_R2_001	4,052,653	151 bp	49%														3.2%	18%
SYN009.I0101.SG1.1_S0_L004_R1_001	3,981,101	151 bp	49%		99.5%	3,966,558	115 bp	47%									3.2%	18%					7,907,972	2.7%	9%
SYN009.I0101.SG1.1_S0_L004_R2_001	3,981,101	151 bp	49%														3.2%	18%
SYN009.I0101_L1_polyg				47.7%															1.2%	78.9%	914.0	99.8%
SYN009.I0101_L2_polyg				47.8%															1.2%	79.1%	907.3	99.8%
SYN009.I0101_L3_polyg				48.1%															1.2%	76.8%	914.1	99.8%
SYN009.I0101_L4_polyg				47.9%															1.2%	78.6%	919.1	99.8%
SYN012.I0101									44.1%	14,614,461	6,273	6,273	0.04	6,273	0.04	83.8%										20.6%	31.0%
SYN012.I0101.SG1.1_S0_L001_R1_001	3,570,228	151 bp	48%		98.2%	3,637,867	139 bp	46%									3.4%	9%					7,003,876	3.0%	18%
SYN012.I0101.SG1.1_S0_L001_R2_001	3,570,228	151 bp	47%														3.3%	18%
SYN012.I0101.SG1.1_S0_L002_R1_001	3,523,198	151 bp	48%		98.2%	3,590,788	139 bp	46%									3.3%	9%					6,903,186	2.9%	18%
SYN012.I0101.SG1.1_S0_L002_R2_001	3,523,198	151 bp	47%														3.4%	18%
SYN012.I0101.SG1.1_S0_L003_R1_001	3,647,244	151 bp	48%		98.0%	3,722,204	139 bp	46%									3.5%	9%					7,140,222	3.1%	18%
SYN012.I0101.SG1.1_S0_L003_R2_001	3,647,244	151 bp	47%														3.6%	18%
SYN012.I0101.SG1.1_S0_L004_R1_001	3,595,317	151 bp	48%		98.2%	3,663,602	139 bp	46%									3.6%	9%					7,044,228	3.2%	18%
SYN012.I0101.SG1.1_S0_L004_R2_001	3,595,317	151 bp	47%														3.6%	18%
SYN012.I0101_L1_polyg				46.8%															1.2%	80.9%	855.6	99.9%
SYN012.I0101_L2_polyg				46.8%															1.2%	81.1%	846.0	99.8%
SYN012.I0101_L3_polyg				47.1%															1.2%	78.7%	849.8	99.9%
SYN012.I0101_L4_polyg				46.9%															1.2%	80.6%	858.0	99.8%
SYN013.I0101									32.7%	12,471,967	5,434	5,434	0.04	5,434	0.04	77.8%										16.2%	42.0%
SYN013.I0101.SG1.1_S0_L001_R1_001	3,353,735	151 bp	45%		99.5%	3,342,234	114 bp	41%									4.3%	18%					6,665,532	3.4%	9%
SYN013.I0101.SG1.1_S0_L001_R2_001	3,353,735	151 bp	44%														4.1%	18%
SYN013.I0101.SG1.1_S0_L002_R1_001	3,289,052	151 bp	45%		99.5%	3,276,953	114 bp	41%									4.3%	18%					6,528,302	3.3%	9%
SYN013.I0101.SG1.1_S0_L002_R2_001	3,289,052	151 bp	44%														4.0%	18%
SYN013.I0101.SG1.1_S0_L003_R1_001	3,430,939	151 bp	45%		99.5%	3,420,830	114 bp	41%									4.4%	18%					6,813,878	3.6%	9%
SYN013.I0101.SG1.1_S0_L003_R2_001	3,430,939	151 bp	44%														4.2%	18%
SYN013.I0101.SG1.1_S0_L004_R1_001					99.5%	2,431,950	114 bp	41%															4,845,836	2.8%	9%
SYN013.I0101.SG1.1_S0_L004_R2_001	3,377,921	151 bp	44%														4.2%	18%
SYN013.I0101_L1_polyg				43.4%															1.2%	78.9%	776.0	99.8%
SYN013.I0101_L2_polyg				43.4%															1.2%	79.0%	760.8	99.8%
SYN013.I0101_L3_polyg				43.7%															1.2%	76.7%	770.7	99.8%
SYN013.I0101_L4_polyg				43.6%															1.1%	78.5%	561.5	99.8%
SYN014.A0101									14.0%	14,216,100	7,809	7,809	0.05	7,809	0.05	72.5%										62.7%	67.0%
SYN014.A0101.SG1.1_S0_L001_R1_001	3,543,227	151 bp	43%		99.4%	3,542,519	125 bp	40%									12.8%	9%					7,031,674	10.5%	9%
SYN014.A0101.SG1.1_S0_L001_R2_001	3,543,227	151 bp	43%														12.2%	18%
SYN014.A0101.SG1.1_S0_L002_R1_001	3,490,571	151 bp	43%		99.4%	3,488,380	125 bp	40%									12.5%	9%					6,919,050	10.2%	9%
SYN014.A0101.SG1.1_S0_L002_R2_001	3,490,571	151 bp	43%														11.8%	18%
SYN014.A0101.SG1.1_S0_L003_R1_001	3,628,491	151 bp	43%		99.4%	3,628,404	124 bp	40%									12.9%	9%					7,195,784	10.6%	9%
SYN014.A0101.SG1.1_S0_L003_R2_001	3,628,491	151 bp	43%														12.4%	18%
SYN014.A0101.SG1.1_S0_L004_R1_001	3,559,805	151 bp	43%		99.4%	3,556,797	124 bp	40%									13.0%	9%					7,057,682	10.5%	9%
SYN014.A0101.SG1.1_S0_L004_R2_001	3,559,805	151 bp	43%														12.2%	18%
SYN014.A0101_L1_polyg				42.2%															1.6%	81.6%	852.0	99.8%
SYN014.A0101_L2_polyg				42.2%															1.6%	81.7%	840.7	99.7%
SYN014.A0101_L3_polyg				42.4%															1.6%	79.3%	847.6	99.8%
SYN014.A0101_L4_polyg				42.3%															1.6%	81.3%	852.2	99.7%
SYN014.C0101									20.7%	12,555,540	5,451	5,451	0.04	5,451	0.04	82.8%										58.8%	61.6%
SYN014.C0101.SG1.1_S0_L001_R1_001	3,117,954	151 bp	45%		99.4%	3,122,244	124 bp	43%									10.7%	9%					6,191,702	8.7%	9%
SYN014.C0101.SG1.1_S0_L001_R2_001	3,117,954	151 bp	44%														10.7%	18%
SYN014.C0101.SG1.1_S0_L002_R1_001	3,080,716	151 bp	45%		99.4%	3,084,787	125 bp	43%									10.5%	9%					6,116,482	8.5%	9%
SYN014.C0101.SG1.1_S0_L002_R2_001	3,080,716	151 bp	44%														10.2%	18%
SYN014.C0101.SG1.1_S0_L003_R1_001	3,202,841	151 bp	45%		99.4%	3,208,712	124 bp	43%									10.8%	9%					6,355,442	8.8%	9%
SYN014.C0101.SG1.1_S0_L003_R2_001	3,202,841	151 bp	44%														11.0%	18%
SYN014.C0101.SG1.1_S0_L004_R1_001	3,135,618	151 bp	45%		99.4%	3,139,797	124 bp	43%									11.1%	9%					6,225,524	9.0%	9%
SYN014.C0101.SG1.1_S0_L004_R2_001	3,135,618	151 bp	44%														10.7%	18%
SYN014.C0101_L1_polyg				43.7%															1.4%	81.3%	747.2	99.9%
SYN014.C0101_L2_polyg				43.7%															1.4%	81.4%	739.8	99.8%
SYN014.C0101_L3_polyg				43.9%															1.4%	78.9%	744.9	99.9%
SYN014.C0101_L4_polyg				43.8%															1.4%	80.9%	748.3	99.8%
SYN015.B0101									24.4%	14,246,779	9,688	9,688	0.07	9,688	0.07	59.5%										27.7%	40.7%
SYN015.B0101.SG1.1_S0_L001_R1_001	3,543,527	151 bp	46%		99.3%	3,544,394	129 bp	42%									5.2%	18%					7,019,808	4.4%	9%
SYN015.B0101.SG1.1_S0_L001_R2_001	3,543,527	151 bp	45%														4.9%	18%
SYN015.B0101.SG1.1_S0_L002_R1_001	3,500,733	151 bp	46%		99.2%	3,502,046	129 bp	42%									5.0%	18%					6,926,670	4.2%	9%
SYN015.B0101.SG1.1_S0_L002_R2_001	3,500,733	151 bp	45%														4.8%	18%
SYN015.B0101.SG1.1_S0_L003_R1_001	3,627,276	151 bp	46%		99.2%	3,630,864	128 bp	42%									5.2%	18%					7,177,312	4.5%	9%
SYN015.B0101.SG1.1_S0_L003_R2_001	3,627,276	151 bp	45%														5.1%	18%
SYN015.B0101.SG1.1_S0_L004_R1_001	3,569,013	151 bp	46%		99.2%	3,569,475	129 bp	42%									5.3%	18%					7,062,238	4.5%	9%
SYN015.B0101.SG1.1_S0_L004_R2_001	3,569,013	151 bp	45%														5.0%	18%
SYN015.B0101_L1_polyg				44.5%															1.8%	79.3%	828.1	99.8%
SYN015.B0101_L2_polyg				44.6%															1.7%	79.5%	820.1	99.7%
SYN015.B0101_L3_polyg				44.8%															1.8%	77.5%	827.8	99.8%
SYN015.B0101_L4_polyg				44.7%															1.8%	79.2%	832.2	99.7%
SYN015.D0101									54.5%	10,790,895	6,042	6,042	0.06	6,042	0.06	69.0%										9.2%	24.2%
SYN015.D0101.SG1.1_S0_L001_R1_001	2,702,420	151 bp	49%		99.0%	2,697,759	126 bp	47%									6.3%	18%					5,339,922	4.9%	9%
SYN015.D0101.SG1.1_S0_L001_R2_001	2,702,420	151 bp	49%														6.1%	18%
SYN015.D0101.SG1.1_S0_L002_R1_001	2,644,226	151 bp	49%		98.9%	2,640,060	126 bp	47%									6.1%	18%					5,222,538	4.7%	9%
SYN015.D0101.SG1.1_S0_L002_R2_001	2,644,226	151 bp	49%														5.9%	18%
SYN015.D0101.SG1.1_S0_L003_R1_001	2,767,982	151 bp	50%		98.8%	2,766,182	126 bp	47%									6.4%	18%					5,460,166	5.0%	9%
SYN015.D0101.SG1.1_S0_L003_R2_001	2,767,982	151 bp	49%														6.2%	18%
SYN015.D0101.SG1.1_S0_L004_R1_001	2,691,401	151 bp	49%		99.0%	2,686,894	126 bp	47%									6.3%	18%					5,315,838	4.9%	9%
SYN015.D0101.SG1.1_S0_L004_R2_001	2,691,401	151 bp	49%														6.0%	18%
SYN015.D0101_L1_polyg				47.6%															1.5%	78.7%	620.1	99.8%
SYN015.D0101_L2_polyg				47.7%															1.4%	78.8%	608.0	99.8%
SYN015.D0101_L3_polyg				48.0%															1.4%	76.5%	617.7	99.8%
SYN015.D0101_L4_polyg				47.9%															1.4%	78.3%	614.6	99.8%
SYN015.E0101									65.1%	9,018,395	7,706	7,706	0.09	7,706	0.09	61.8%										6.6%	11.8%
SYN015.E0101.SG1.1_S0_L001_R1_001	2,434,156	151 bp	53%		99.3%	2,244,620	93 bp	47%									9.5%	18%					4,822,184	6.4%	9%
SYN015.E0101.SG1.1_S0_L001_R2_001	2,434,156	151 bp	52%														9.3%	27%
SYN015.E0101.SG1.1_S0_L002_R1_001	2,391,382	151 bp	53%		99.2%	2,207,763	93 bp	47%									9.4%	18%					4,732,850	6.3%	9%
SYN015.E0101.SG1.1_S0_L002_R2_001	2,391,382	151 bp	52%														9.0%	27%
SYN015.E0101.SG1.1_S0_L003_R1_001	2,509,659	151 bp	54%		99.2%	2,314,252	93 bp	47%									9.7%	18%					4,968,076	6.8%	9%
SYN015.E0101.SG1.1_S0_L003_R2_001	2,509,659	151 bp	52%														9.5%	27%
SYN015.E0101.SG1.1_S0_L004_R1_001	2,440,290	151 bp	53%		99.2%	2,251,760	93 bp	47%									9.6%	18%					4,830,568	6.5%	9%
SYN015.E0101.SG1.1_S0_L004_R2_001	2,440,290	151 bp	52%														9.3%	27%
SYN015.E0101_L1_polyg				47.9%															2.8%	75.8%	501.5	99.8%
SYN015.E0101_L2_polyg				48.0%															2.8%	75.7%	492.4	99.7%
SYN015.E0101_L3_polyg				48.6%															2.8%	73.1%	498.2	99.8%
SYN015.E0101_L4_polyg				48.3%															2.8%	75.0%	497.2	99.7%
SYN015.F0101									36.8%	14,526,224	9,625	9,625	0.07	9,625	0.07	56.1%										23.6%	37.9%
SYN015.F0101.SG1.1_S0_L001_R1_001	3,661,829	151 bp	47%		99.0%	3,611,359	124 bp	45%									4.5%	18%					7,233,432	3.8%	9%
SYN015.F0101.SG1.1_S0_L001_R2_001	3,661,829	151 bp	46%														4.5%	18%
SYN015.F0101.SG1.1_S0_L002_R1_001	3,621,190	151 bp	47%		98.9%	3,573,360	124 bp	45%									4.6%	18%					7,149,320	3.8%	9%
SYN015.F0101.SG1.1_S0_L002_R2_001	3,621,190	151 bp	46%														4.4%	18%
SYN015.F0101.SG1.1_S0_L003_R1_001	3,750,710	151 bp	47%		98.9%	3,701,440	124 bp	45%									4.6%	18%					7,399,540	3.9%	9%
SYN015.F0101.SG1.1_S0_L003_R2_001	3,750,710	151 bp	46%														4.6%	18%
SYN015.F0101.SG1.1_S0_L004_R1_001	3,689,783	151 bp	47%		98.9%	3,640,065	124 bp	45%									4.8%	18%					7,283,600	4.1%	9%
SYN015.F0101.SG1.1_S0_L004_R2_001	3,689,783	151 bp	46%														4.7%	18%
SYN015.F0101_L1_polyg				44.8%															1.7%	81.1%	858.7	99.8%
SYN015.F0101_L2_polyg				44.8%															1.7%	81.2%	850.4	99.8%
SYN015.F0101_L3_polyg				45.0%															1.7%	78.5%	850.6	99.8%
SYN015.F0101_L4_polyg				44.9%															1.8%	80.6%	859.5	99.8%
SYN015.G0101									17.2%	12,814,375	7,009	7,009	0.05	7,009	0.05	64.8%										34.3%	69.2%
SYN015.G0101.SG1.1_S0_L001_R1_001	3,209,970	151 bp	43%		99.3%	3,198,393	125 bp	40%									8.0%	9%					6,363,212	6.5%	9%
SYN015.G0101.SG1.1_S0_L001_R2_001	3,209,970	151 bp	43%														7.4%	18%
SYN015.G0101.SG1.1_S0_L002_R1_001	3,149,076	151 bp	43%		99.3%	3,137,769	125 bp	40%									7.8%	9%					6,235,486	6.3%	9%
SYN015.G0101.SG1.1_S0_L002_R2_001	3,149,076	151 bp	43%														7.0%	18%
SYN015.G0101.SG1.1_S0_L003_R1_001	3,280,448	151 bp	43%		99.2%	3,269,709	125 bp	40%									8.0%	9%					6,498,108	6.5%	9%
SYN015.G0101.SG1.1_S0_L003_R2_001	3,280,448	151 bp	43%														7.5%	18%
SYN015.G0101.SG1.1_S0_L004_R1_001	3,220,926	151 bp	43%		99.3%	3,208,504	125 bp	40%									8.2%	9%					6,379,786	6.7%	9%
SYN015.G0101.SG1.1_S0_L004_R2_001	3,220,926	151 bp	43%														7.5%	18%
SYN015.G0101_L1_polyg				41.9%															1.3%	80.7%	757.8	99.8%
SYN015.G0101_L2_polyg				41.9%															1.3%	80.9%	745.3	99.7%
SYN015.G0101_L3_polyg				42.0%															1.3%	78.5%	753.6	99.8%
SYN015.G0101_L4_polyg				41.9%															1.4%	80.5%	758.6	99.7%
SYN015.H0101									19.1%	15,108,690	9,098	9,098	0.06	9,098	0.06	63.6%										27.4%	60.0%
SYN015.H0101.SG1.1_S0_L001_R1_001	3,793,125	151 bp	45%		99.5%	3,777,380	113 bp	40%									7.7%	18%					7,536,634	6.2%	9%
SYN015.H0101.SG1.1_S0_L001_R2_001	3,793,125	151 bp	43%														7.4%	18%
SYN015.H0101.SG1.1_S0_L002_R1_001	3,708,409	151 bp	45%		99.5%	3,687,781	114 bp	40%									7.7%	18%					7,347,882	6.0%	9%
SYN015.H0101.SG1.1_S0_L002_R2_001	3,708,409	151 bp	44%														7.3%	18%
SYN015.H0101.SG1.1_S0_L003_R1_001	3,891,367	151 bp	45%		99.5%	3,876,620	113 bp	40%									7.9%	18%					7,727,728	6.3%	9%
SYN015.H0101.SG1.1_S0_L003_R2_001	3,891,367	151 bp	44%														7.6%	18%
SYN015.H0101.SG1.1_S0_L004_R1_001	3,788,027	151 bp	45%		99.5%	3,766,909	113 bp	40%									7.9%	18%					7,508,246	6.3%	9%
SYN015.H0101.SG1.1_S0_L004_R2_001	3,788,027	151 bp	44%														7.6%	18%
SYN015.H0101_L1_polyg				43.0%															1.5%	78.7%	875.4	99.8%
SYN015.H0101_L2_polyg				43.1%															1.4%	78.8%	855.2	99.6%
SYN015.H0101_L3_polyg				43.4%															1.5%	76.9%	877.0	99.8%
SYN015.H0101_L4_polyg				43.2%															1.5%	78.5%	870.2	99.6%
SYN015.I0101									46.3%	14,620,185	7,201	7,201	0.05	7,201	0.05	74.8%										9.4%	31.0%
SYN015.I0101.SG1.1_S0_L001_R1_001	3,580,273	151 bp	48%		98.4%	3,633,680	141 bp	46%									3.7%	9%					7,040,152	3.2%	9%
SYN015.I0101.SG1.1_S0_L001_R2_001	3,580,273	151 bp	48%														3.7%	18%
SYN015.I0101.SG1.1_S0_L002_R1_001	3,535,158	151 bp	48%		98.4%	3,589,018	141 bp	47%									3.6%	9%					6,942,626	3.2%	9%
SYN015.I0101.SG1.1_S0_L002_R2_001	3,535,158	151 bp	48%														3.6%	18%
SYN015.I0101.SG1.1_S0_L003_R1_001	3,674,014	151 bp	48%		98.3%	3,734,051	140 bp	47%									3.8%	9%					7,209,924	3.4%	9%
SYN015.I0101.SG1.1_S0_L003_R2_001	3,674,014	151 bp	48%														3.8%	18%
SYN015.I0101.SG1.1_S0_L004_R1_001	3,608,926	151 bp	48%		98.4%	3,663,436	141 bp	47%									3.7%	9%					7,086,588	3.4%	9%
SYN015.I0101.SG1.1_S0_L004_R2_001	3,608,926	151 bp	48%														3.8%	18%
SYN015.I0101_L1_polyg				47.3%															1.2%	80.6%	854.4	99.9%
SYN015.I0101_L2_polyg				47.4%															1.2%	80.8%	845.8	99.8%
SYN015.I0101_L3_polyg				47.7%															1.2%	78.5%	853.9	99.9%
SYN015.I0101_L4_polyg				47.5%															1.2%	80.4%	858.4	99.8%
SYN016.I0101									39.4%	13,611,033	6,745	6,745	0.05	6,745	0.05	73.2%										17.3%	40.0%
SYN016.I0101.SG1.1_S0_L001_R1_001	3,393,714	151 bp	46%		99.4%	3,387,909	118 bp	44%									4.2%	18%					6,734,882	3.3%	18%
SYN016.I0101.SG1.1_S0_L001_R2_001	3,393,714	151 bp	47%														4.1%	27%
SYN016.I0101.SG1.1_S0_L002_R1_001	3,338,917	151 bp	46%		99.4%	3,333,834	118 bp	44%									4.0%	18%					6,624,768	3.3%	18%
SYN016.I0101.SG1.1_S0_L002_R2_001	3,338,917	151 bp	47%														3.9%	27%
SYN016.I0101.SG1.1_S0_L003_R1_001	3,489,146	151 bp	47%		99.3%	3,486,174	117 bp	44%									4.3%	27%					6,916,198	3.5%	18%
SYN016.I0101.SG1.1_S0_L003_R2_001	3,489,146	151 bp	47%														4.3%	27%
SYN016.I0101.SG1.1_S0_L004_R1_001	3,407,948	151 bp	47%		99.4%	3,403,116	118 bp	44%									4.3%	18%					6,759,838	3.5%	18%
SYN016.I0101.SG1.1_S0_L004_R2_001	3,407,948	151 bp	47%														4.2%	27%
SYN016.I0101_L1_polyg				45.5%															1.6%	80.5%	801.0	99.8%
SYN016.I0101_L2_polyg				45.6%															1.6%	80.7%	790.4	99.8%
SYN016.I0101_L3_polyg				45.8%															1.6%	78.0%	797.7	99.8%
SYN016.I0101_L4_polyg				45.6%															1.7%	80.1%	800.6	99.8%
SYN017.A0101									20.4%	14,050,397	6,704	6,704	0.05	6,704	0.05	78.8%										0.0%	15.6%
SYN017.A0101.SG1.1_S0_L001_R1_001	3,485,347	151 bp	45%		99.4%	3,494,330	131 bp	43%									3.4%	9%					6,917,808	3.0%	9%
SYN017.A0101.SG1.1_S0_L001_R2_001	3,485,347	151 bp	45%														3.6%	18%
SYN017.A0101.SG1.1_S0_L002_R1_001	3,442,859	151 bp	45%		99.3%	3,452,416	131 bp	43%									3.5%	9%					6,830,522	3.0%	9%
SYN017.A0101.SG1.1_S0_L002_R2_001	3,442,859	151 bp	45%														3.4%	18%
SYN017.A0101.SG1.1_S0_L003_R1_001	3,571,784	151 bp	45%		99.3%	3,583,423	131 bp	43%									3.6%	9%					7,082,970	3.2%	9%
SYN017.A0101.SG1.1_S0_L003_R2_001	3,571,784	151 bp	45%														3.7%	18%
SYN017.A0101.SG1.1_S0_L004_R1_001	3,511,162	151 bp	45%		99.4%	3,520,228	131 bp	43%									3.6%	9%					6,966,616	3.2%	9%
SYN017.A0101.SG1.1_S0_L004_R2_001	3,511,162	151 bp	45%														3.7%	18%
SYN017.A0101_L1_polyg				44.4%															1.2%	81.7%	843.2	99.9%
SYN017.A0101_L2_polyg				44.4%															1.2%	82.0%	835.3	99.9%
SYN017.A0101_L3_polyg				44.6%															1.2%	79.4%	839.5	99.9%
SYN017.A0101_L4_polyg				44.5%															1.2%	81.5%	846.6	99.8%
SYN017.B0101									20.5%	12,487,099	5,479	5,479	0.04	5,479	0.04	82.9%										0.0%	26.6%
SYN017.B0101.SG1.1_S0_L001_R1_001	3,632,902	151 bp	44%		99.1%	3,658,418	136 bp	42%									4.7%	9%					7,189,648	4.0%	9%
SYN017.B0101.SG1.1_S0_L001_R2_001	3,632,902	151 bp	44%														4.6%	18%
SYN017.B0101.SG1.1_S0_L002_R1_001	3,586,265	151 bp	44%		99.1%	3,612,265	137 bp	42%									4.7%	9%					7,095,596	4.0%	9%
SYN017.B0101.SG1.1_S0_L002_R2_001	3,586,265	151 bp	44%														4.6%	18%
SYN017.B0101.SG1.1_S0_L003_R1_001	3,706,808	151 bp	44%		99.0%	3,734,565	136 bp	42%									4.8%	9%					7,328,956	4.2%	9%
SYN017.B0101.SG1.1_S0_L003_R2_001	3,706,808	151 bp	44%														4.7%	18%
SYN017.B0101.SG1.1_S0_L004_R1_001	3,651,689	151 bp	44%		99.1%	1,481,851	137 bp	42%									4.9%	9%					2,911,896	2.1%	9%
SYN017.B0101_L1_polyg				43.8%															1.2%	82.0%	882.5	99.9%
SYN017.B0101_L2_polyg				43.8%															1.2%	82.3%	874.5	99.9%
SYN017.B0101_L3_polyg				43.9%															1.2%	80.0%	877.5	99.9%
SYN017.B0101_L4_polyg				43.8%															1.0%	82.3%	358.9	99.9%
SYN017.D0101									49.3%	8,083,229	3,429	3,429	0.04	3,429	0.04	83.6%										29.0%	32.9%
SYN017.D0101.SG1.1_S0_L001_R1_001	1,997,426	151 bp	47%		99.0%	2,013,921	134 bp	46%									3.5%	9%					3,948,546	3.0%	18%
SYN017.D0101.SG1.1_S0_L001_R2_001	1,997,426	151 bp	47%														3.5%	18%
SYN017.D0101.SG1.1_S0_L002_R1_001	1,964,036	151 bp	47%		99.0%	1,979,402	135 bp	46%									3.4%	9%					3,878,560	2.9%	18%
SYN017.D0101.SG1.1_S0_L002_R2_001	1,964,036	151 bp	47%														3.4%	18%
SYN017.D0101.SG1.1_S0_L003_R1_001	2,045,215	151 bp	48%		98.8%	2,064,503	134 bp	46%									3.7%	9%					4,036,894	3.2%	18%
SYN017.D0101.SG1.1_S0_L003_R2_001	2,045,215	151 bp	47%														3.6%	18%
SYN017.D0101.SG1.1_S0_L004_R1_001	2,009,355	151 bp	48%		98.9%	2,025,403	135 bp	46%									3.7%	9%					3,967,954	3.3%	18%
SYN017.D0101.SG1.1_S0_L004_R2_001	2,009,355	151 bp	47%														3.8%	18%
SYN017.D0101_L1_polyg				46.9%															1.1%	80.8%	477.8	99.9%
SYN017.D0101_L2_polyg				46.9%															1.1%	81.1%	470.8	99.8%
SYN017.D0101_L3_polyg				47.1%															1.1%	78.5%	474.5	99.9%
SYN017.D0101_L4_polyg				47.0%															1.1%	80.5%	478.3	99.8%
SYN017.E0101									48.8%	12,505,834	7,029	7,029	0.06	7,029	0.06	67.6%										25.7%	32.1%
SYN017.E0101.SG1.1_S0_L001_R1_001	3,081,377	151 bp	48%		98.7%	3,114,406	136 bp	47%									5.2%	9%					6,076,658	4.4%	9%
SYN017.E0101.SG1.1_S0_L001_R2_001	3,081,377	151 bp	48%														5.0%	18%
SYN017.E0101.SG1.1_S0_L002_R1_001	3,038,493	151 bp	48%		98.7%	3,070,816	136 bp	47%									5.1%	9%					5,985,754	4.3%	9%
SYN017.E0101.SG1.1_S0_L002_R2_001	3,038,493	151 bp	48%														4.8%	18%
SYN017.E0101.SG1.1_S0_L003_R1_001	3,149,306	151 bp	48%		98.6%	3,187,332	135 bp	47%									5.4%	9%					6,199,616	4.6%	9%
SYN017.E0101.SG1.1_S0_L003_R2_001	3,149,306	151 bp	48%														5.3%	18%
SYN017.E0101.SG1.1_S0_L004_R1_001	3,100,144	151 bp	48%		98.7%	3,133,280	136 bp	47%									5.4%	9%					6,106,356	4.7%	9%
SYN017.E0101.SG1.1_S0_L004_R2_001	3,100,144	151 bp	48%														5.2%	18%
SYN017.E0101_L1_polyg				47.5%															1.1%	81.0%	737.4	99.9%
SYN017.E0101_L2_polyg				47.5%															1.1%	81.2%	728.6	99.8%
SYN017.E0101_L3_polyg				47.6%															1.1%	78.7%	731.8	99.8%
SYN017.E0101_L4_polyg				47.6%															1.2%	80.7%	738.7	99.8%
SYN017.F0101									25.1%	13,812,745	6,528	6,528	0.05	6,528	0.05	76.4%										36.3%	60.4%
SYN017.F0101.SG1.1_S0_L001_R1_001	3,417,574	151 bp	44%		99.0%	3,441,586	133 bp	42%									7.0%	9%					6,757,134	5.9%	9%
SYN017.F0101.SG1.1_S0_L001_R2_001	3,417,574	151 bp	44%														6.8%	18%
SYN017.F0101.SG1.1_S0_L002_R1_001	3,368,341	151 bp	44%		99.0%	3,392,898	133 bp	42%									6.8%	9%					6,657,392	5.7%	9%
SYN017.F0101.SG1.1_S0_L002_R2_001	3,368,341	151 bp	44%														6.6%	18%
SYN017.F0101.SG1.1_S0_L003_R1_001	3,490,379	151 bp	44%		98.9%	3,517,122	132 bp	42%									7.0%	9%					6,894,336	6.0%	9%
SYN017.F0101.SG1.1_S0_L003_R2_001	3,490,379	151 bp	44%														7.0%	18%
SYN017.F0101.SG1.1_S0_L004_R1_001	3,437,249	151 bp	44%		99.0%	3,461,139	133 bp	42%									7.2%	9%					6,794,518	6.0%	9%
SYN017.F0101.SG1.1_S0_L004_R2_001	3,437,249	151 bp	44%														6.9%	18%
SYN017.F0101_L1_polyg				43.3%															1.3%	82.1%	829.3	99.9%
SYN017.F0101_L2_polyg				43.3%															1.3%	82.4%	820.2	99.8%
SYN017.F0101_L3_polyg				43.4%															1.3%	80.1%	825.0	99.8%
SYN017.F0101_L4_polyg				43.3%															1.3%	82.1%	833.2	99.8%
SYN017.G0101									16.5%	9,578,283	4,505	4,505	0.05	4,505	0.05	82.8%										25.6%	70.1%
SYN017.G0101.SG1.1_S0_L001_R1_001	2,796,211	151 bp	43%		99.5%	2,796,595	125 bp	40%									7.7%	9%					5,555,728	6.4%	9%
SYN017.G0101.SG1.1_S0_L001_R2_001	2,796,211	151 bp	43%														7.8%	18%
SYN017.G0101.SG1.1_S0_L002_R1_001	2,753,884	151 bp	43%		99.5%	2,752,306	125 bp	40%									7.8%	9%					5,463,078	6.5%	9%
SYN017.G0101.SG1.1_S0_L002_R2_001	2,753,884	151 bp	43%														7.5%	18%
SYN017.G0101.SG1.1_S0_L003_R1_001	2,852,130	151 bp	44%		99.4%	1,219,078	124 bp	40%									7.9%	9%					2,419,858	3.3%	9%
SYN017.G0101.SG1.1_S0_L003_R2_001	1,218,565	151 bp	43%														3.9%	18%
SYN017.G0101.SG1.1_S0_L004_R1_001	2,811,959	151 bp	43%		99.5%	2,810,304	125 bp	40%									7.9%	9%					5,579,292	6.6%	9%
SYN017.G0101.SG1.1_S0_L004_R2_001	2,811,959	151 bp	43%														8.0%	18%
SYN017.G0101_L1_polyg				42.5%															1.2%	81.1%	670.5	99.9%
SYN017.G0101_L2_polyg				42.5%															1.2%	81.3%	660.9	99.7%
SYN017.G0101_L3_polyg				42.8%															1.0%	79.1%	284.5	99.8%
SYN017.G0101_L4_polyg				42.6%															1.2%	81.0%	672.1	99.7%
SYN018.C0101									29.8%	16,248,693	21,821	21,821	0.13	21,821	0.13	39.7%										8.2%	20.2%
SYN018.C0101.SG1.1_S0_L001_R1_001	4,099,481	151 bp	46%		99.0%	4,037,814	123 bp	43%									5.9%	18%					8,090,070	5.0%	9%
SYN018.C0101.SG1.1_S0_L001_R2_001	4,099,481	151 bp	46%														5.9%	18%
SYN018.C0101.SG1.1_S0_L002_R1_001	4,051,626	151 bp	46%		99.0%	3,994,093	124 bp	43%									5.8%	18%					7,993,412	5.0%	9%
SYN018.C0101.SG1.1_S0_L002_R2_001	4,051,626	151 bp	46%														5.7%	18%
SYN018.C0101.SG1.1_S0_L003_R1_001	4,206,372	151 bp	47%		98.9%	4,143,536	123 bp	43%									5.9%	18%					8,293,730	5.2%	9%
SYN018.C0101.SG1.1_S0_L003_R2_001	4,206,372	151 bp	46%														6.1%	18%
SYN018.C0101.SG1.1_S0_L004_R1_001	4,133,561	151 bp	46%		99.0%	4,073,250	123 bp	43%									6.1%	18%					8,154,984	5.3%	9%
SYN018.C0101.SG1.1_S0_L004_R2_001	4,133,561	151 bp	46%														6.1%	18%
SYN018.C0101_L1_polyg				44.3%															3.5%	80.5%	952.6	99.7%
SYN018.C0101_L2_polyg				44.3%															3.5%	80.7%	944.2	99.7%
SYN018.C0101_L3_polyg				44.5%															3.6%	78.2%	948.9	99.6%
SYN018.C0101_L4_polyg				44.4%															3.6%	80.2%	956.9	99.7%
SYN018.H0101									26.1%	14,987,668	8,242	8,242	0.05	8,242	0.05	70.4%										15.6%	58.6%
SYN018.H0101.SG1.1_S0_L001_R1_001	3,731,093	151 bp	44%		99.5%	3,723,656	122 bp	40%									8.5%	9%					7,410,160	7.0%	9%
SYN018.H0101.SG1.1_S0_L001_R2_001	3,731,093	151 bp	43%														8.2%	18%
SYN018.H0101.SG1.1_S0_L002_R1_001	3,693,993	151 bp	44%		99.5%	3,685,986	122 bp	40%									8.4%	9%					7,329,502	6.8%	9%
SYN018.H0101.SG1.1_S0_L002_R2_001	3,693,993	151 bp	43%														7.9%	18%
SYN018.H0101.SG1.1_S0_L003_R1_001	3,826,284	151 bp	44%		99.4%	3,819,117	122 bp	40%									8.6%	18%					7,594,814	7.1%	9%
SYN018.H0101.SG1.1_S0_L003_R2_001	3,826,284	151 bp	43%														8.3%	18%
SYN018.H0101.SG1.1_S0_L004_R1_001	3,768,126	151 bp	44%		99.5%	3,758,909	122 bp	40%									8.7%	9%					7,477,382	7.1%	9%
SYN018.H0101.SG1.1_S0_L004_R2_001	3,768,126	151 bp	43%														8.3%	18%
SYN018.H0101_L1_polyg				42.7%															1.7%	79.6%	873.7	99.8%
SYN018.H0101_L2_polyg				42.8%															1.7%	79.8%	867.1	99.8%
SYN018.H0101_L3_polyg				43.0%															1.7%	77.7%	874.4	99.8%
SYN018.H0101_L4_polyg				42.9%															1.7%	79.4%	880.6	99.7%
SYN018.I0101									20.6%	14,014,214	4,958	4,958	0.04	4,958	0.04	85.2%										16.4%	33.8%
SYN018.I0101.SG1.1_S0_L001_R1_001	3,227,126	151 bp	42%		93.9%	3,494,059	156 bp	40%									5.8%	9%					6,054,246	5.5%	9%
SYN018.I0101.SG1.1_S0_L001_R2_001	3,227,126	151 bp	42%														5.7%	9%
SYN018.I0101.SG1.1_S0_L002_R1_001	3,185,014	151 bp	42%		93.8%	3,450,358	157 bp	40%									5.8%	9%					5,968,506	5.4%	0%
SYN018.I0101.SG1.1_S0_L002_R2_001	3,185,014	151 bp	42%														5.6%	9%
SYN018.I0101.SG1.1_S0_L003_R1_001	3,284,013	151 bp	42%		93.8%	3,556,258	156 bp	40%									5.9%	9%					6,153,592	5.7%	9%
SYN018.I0101.SG1.1_S0_L003_R2_001	3,284,013	151 bp	42%														5.8%	9%
SYN018.I0101.SG1.1_S0_L004_R1_001	3,246,729	151 bp	42%		94.0%	3,513,539	156 bp	40%									6.0%	9%					6,091,506	5.7%	9%
SYN018.I0101.SG1.1_S0_L004_R2_001	3,246,729	151 bp	42%														5.8%	9%
SYN018.I0101_L1_polyg				41.7%															1.1%	82.5%	793.1	99.9%
SYN018.I0101_L2_polyg				41.7%															1.1%	82.8%	785.0	99.8%
SYN018.I0101_L3_polyg				41.8%															1.1%	80.5%	787.0	99.9%
SYN018.I0101_L4_polyg				41.7%															1.1%	82.4%	796.9	99.8%
SYN019.I0101									42.7%	13,908,460	6,426	6,426	0.05	6,426	0.05	75.8%										14.4%	34.7%
SYN019.I0101.SG1.1_S0_L001_R1_001	3,460,838	151 bp	49%		99.2%	3,459,274	125 bp	47%									2.8%	18%					6,856,540	2.4%	9%
SYN019.I0101.SG1.1_S0_L001_R2_001	3,460,838	151 bp	48%														2.9%	18%
SYN019.I0101.SG1.1_S0_L002_R1_001	3,409,491	151 bp	49%		99.2%	3,409,509	125 bp	47%									2.7%	18%					6,752,382	2.3%	9%
SYN019.I0101.SG1.1_S0_L002_R2_001	3,409,491	151 bp	48%														2.8%	18%
SYN019.I0101.SG1.1_S0_L003_R1_001	3,554,111	151 bp	49%		99.1%	3,556,789	125 bp	47%									3.0%	18%					7,030,084	2.5%	9%
SYN019.I0101.SG1.1_S0_L003_R2_001	3,554,111	151 bp	48%														3.0%	18%
SYN019.I0101.SG1.1_S0_L004_R1_001	3,482,559	151 bp	49%		99.2%	3,482,888	125 bp	47%									3.0%	18%					6,895,838	2.5%	9%
SYN019.I0101.SG1.1_S0_L004_R2_001	3,482,559	151 bp	48%														3.0%	18%
SYN019.I0101_L1_polyg				47.5%															1.1%	79.5%	806.6	99.9%
SYN019.I0101_L2_polyg				47.5%															1.1%	79.6%	796.6	99.8%
SYN019.I0101_L3_polyg				47.9%															1.1%	77.0%	802.9	99.8%
SYN019.I0101_L4_polyg				47.7%															1.2%	79.0%	807.5	99.8%
SYN021.I0101									21.6%	12,163,034	4,715	4,715	0.04	4,715	0.04	74.1%										37.4%	56.5%
SYN021.I0101.SG1.1_S0_L001_R1_001	3,030,259	151 bp	45%		99.0%	3,044,181	130 bp	43%									5.5%	18%					5,994,992	4.7%	9%
SYN021.I0101.SG1.1_S0_L001_R2_001	3,030,259	151 bp	45%														5.6%	27%
SYN021.I0101.SG1.1_S0_L002_R1_001	2,943,956	151 bp	45%		99.0%	2,958,137	130 bp	43%									5.4%	9%					5,820,516	4.5%	18%
SYN021.I0101.SG1.1_S0_L002_R2_001	2,943,956	151 bp	45%														5.3%	27%
SYN021.I0101.SG1.1_S0_L003_R1_001	3,128,191	151 bp	45%		98.9%	3,145,416	130 bp	43%									5.7%	18%					6,180,280	4.8%	18%
SYN021.I0101.SG1.1_S0_L003_R2_001	3,128,191	151 bp	45%														5.7%	27%
SYN021.I0101.SG1.1_S0_L004_R1_001	3,001,132	151 bp	45%		99.0%	3,015,300	130 bp	43%									5.6%	9%					5,933,138	4.7%	9%
SYN021.I0101.SG1.1_S0_L004_R2_001	3,001,132	151 bp	45%														5.5%	27%
SYN021.I0101_L1_polyg				44.1%															1.1%	80.7%	721.2	99.9%
SYN021.I0101_L2_polyg				44.1%															1.1%	80.8%	702.0	99.8%
SYN021.I0101_L3_polyg				44.2%															1.1%	78.4%	723.2	99.9%
SYN021.I0101_L4_polyg				44.1%															1.1%	80.4%	711.1	99.8%
SYN022.I0101									35.8%	14,148,991	6,479	6,479	0.05	6,479	0.05	80.7%										8.3%	40.5%
SYN022.I0101.SG1.1_S0_L001_R1_001	3,520,014	151 bp	47%		99.3%	3,514,111	126 bp	46%									3.3%	9%					6,979,352	2.8%	9%
SYN022.I0101.SG1.1_S0_L001_R2_001	3,520,014	151 bp	47%														3.4%	18%
SYN022.I0101.SG1.1_S0_L002_R1_001	3,479,886	151 bp	47%		99.3%	3,475,424	126 bp	46%									3.3%	9%					6,896,382	2.7%	9%
SYN022.I0101.SG1.1_S0_L002_R2_001	3,479,886	151 bp	47%														3.2%	18%
SYN022.I0101.SG1.1_S0_L003_R1_001	3,613,532	151 bp	47%		99.2%	3,610,610	126 bp	46%									3.5%	9%					7,155,550	3.0%	9%
SYN022.I0101.SG1.1_S0_L003_R2_001	3,613,532	151 bp	47%														3.5%	18%
SYN022.I0101.SG1.1_S0_L004_R1_001	3,554,142	151 bp	47%		99.3%	3,548,846	126 bp	46%									3.5%	9%					7,043,370	2.9%	9%
SYN022.I0101.SG1.1_S0_L004_R2_001	3,554,142	151 bp	47%														3.5%	18%
SYN022.I0101_L1_polyg				46.1%															1.2%	80.4%	831.3	99.9%
SYN022.I0101_L2_polyg				46.1%															1.2%	80.6%	823.5	99.8%
SYN022.I0101_L3_polyg				46.4%															1.2%	78.1%	828.1	99.8%
SYN022.I0101_L4_polyg				46.2%															1.2%	80.0%	835.3	99.8%
SYN023.I0101									47.3%	15,230,369	4,952	4,952	0.03	4,952	0.03	89.5%										3.1%	20.5%
SYN023.I0101.SG1.1_S0_L001_R1_001	3,203,812	151 bp	45%		85.7%	3,804,420	160 bp	44%									3.4%	9%					5,486,252	3.5%	9%
SYN023.I0101.SG1.1_S0_L001_R2_001	3,203,812	151 bp	45%														3.3%	9%
SYN023.I0101.SG1.1_S0_L002_R1_001	3,152,254	151 bp	45%		85.6%	3,749,154	160 bp	44%									3.3%	9%					5,388,004	3.4%	9%
SYN023.I0101.SG1.1_S0_L002_R2_001	3,152,254	151 bp	45%														3.2%	9%
SYN023.I0101.SG1.1_S0_L003_R1_001	3,261,683	151 bp	45%		85.6%	3,874,002	160 bp	45%									3.5%	9%					5,576,452	3.6%	9%
SYN023.I0101.SG1.1_S0_L003_R2_001	3,261,683	151 bp	45%														3.5%	9%
SYN023.I0101.SG1.1_S0_L004_R1_001	3,204,914	151 bp	45%		85.8%	3,802,793	160 bp	44%									3.5%	9%					5,491,594	3.7%	9%
SYN023.I0101.SG1.1_S0_L004_R2_001	3,204,914	151 bp	45%														3.5%	9%
SYN023.I0101_L1_polyg				44.9%															1.0%	81.9%	783.5	99.9%
SYN023.I0101_L2_polyg				44.9%															1.0%	82.2%	773.2	99.9%
SYN023.I0101_L3_polyg				45.0%															1.0%	79.8%	776.6	99.9%
SYN023.I0101_L4_polyg				44.9%															1.0%	81.7%	781.9	99.9%
SYN025.I0101									43.3%	18,307,538	9,983	9,983	0.05	9,983	0.05	84.3%										6.6%	29.5%
SYN025.I0101.SG1.1_S0_L001_R1_001	4,564,727	151 bp	47%		99.3%	4,557,728	124 bp	46%									3.5%	9%					9,049,532	2.9%	9%
SYN025.I0101.SG1.1_S0_L001_R2_001	4,564,727	151 bp	48%														3.6%	18%
SYN025.I0101.SG1.1_S0_L002_R1_001	4,515,044	151 bp	47%		99.2%	4,489,658	124 bp	46%									3.5%	9%					8,893,608	2.9%	9%
SYN025.I0101.SG1.1_S0_L002_R2_001	4,515,044	151 bp	48%														3.9%	18%
SYN025.I0101.SG1.1_S0_L003_R1_001	4,683,210	151 bp	47%		99.2%	4,680,938	124 bp	46%									3.8%	9%					9,270,762	3.1%	9%
SYN025.I0101.SG1.1_S0_L003_R2_001	4,683,210	151 bp	48%														3.6%	18%
SYN025.I0101.SG1.1_S0_L004_R1_001	4,602,922	151 bp	47%		99.2%	4,579,214	124 bp	46%									3.8%	9%					9,071,740	3.2%	9%
SYN025.I0101.SG1.1_S0_L004_R2_001	4,602,922	151 bp	48%														4.1%	18%
SYN025.I0101_L1_polyg				46.4%															1.2%	80.9%	1,083.7	99.8%
SYN025.I0101_L2_polyg				46.4%															1.2%	81.0%	1,068.1	99.3%
SYN025.I0101_L3_polyg				46.6%															1.2%	78.4%	1,077.4	99.8%
SYN025.I0101_L4_polyg				46.5%															1.2%	80.4%	1,081.0	99.3%
SYN026.I0101									24.2%	14,245,468	4,980	4,980	0.03	4,980	0.03	73.3%										30.1%	49.8%
SYN026.I0101.SG1.1_S0_L001_R1_001	3,539,831	151 bp	45%		99.0%	3,560,272	129 bp	43%									4.9%	9%					7,002,674	4.2%	18%
SYN026.I0101.SG1.1_S0_L001_R2_001	3,539,831	151 bp	45%														4.7%	18%
SYN026.I0101.SG1.1_S0_L002_R1_001	3,457,127	151 bp	45%		99.0%	3,478,791	130 bp	43%									4.7%	9%					6,836,096	4.1%	18%
SYN026.I0101.SG1.1_S0_L002_R2_001	3,457,127	151 bp	45%														4.5%	27%
SYN026.I0101.SG1.1_S0_L003_R1_001	3,653,260	151 bp	46%		98.9%	3,678,298	129 bp	43%									5.0%	18%					7,218,030	4.3%	18%
SYN026.I0101.SG1.1_S0_L003_R2_001	3,653,260	151 bp	45%														5.0%	27%
SYN026.I0101.SG1.1_S0_L004_R1_001	3,507,212	151 bp	45%		99.0%	3,528,107	129 bp	43%									5.0%	9%					6,935,380	4.2%	18%
SYN026.I0101.SG1.1_S0_L004_R2_001	3,507,212	151 bp	45%														4.7%	27%
SYN026.I0101_L1_polyg				44.4%															1.1%	78.3%	818.8	99.9%
SYN026.I0101_L2_polyg				44.5%															1.0%	78.5%	801.7	99.9%
SYN026.I0101_L3_polyg				44.8%															1.1%	76.2%	821.5	99.9%
SYN026.I0101_L4_polyg				44.6%															1.1%	77.9%	806.9	99.8%
SYN028.I0101									38.2%	18,021,868	6,174	6,174	0.03	6,174	0.03	90.4%										3.9%	33.9%
SYN028.I0101.SG1.1_S0_L001_R1_001	3,746,604	151 bp	45%		85.1%	4,479,971	160 bp	45%									3.8%	9%					6,364,904	4.0%	0%
SYN028.I0101.SG1.1_S0_L001_R2_001	3,746,604	151 bp	45%														3.7%	9%
SYN028.I0101.SG1.1_S0_L002_R1_001	3,722,803	151 bp	45%		84.8%	4,458,865	160 bp	45%									3.7%	9%					6,300,798	3.9%	0%
SYN028.I0101.SG1.1_S0_L002_R2_001	3,722,803	151 bp	45%														3.7%	9%
SYN028.I0101.SG1.1_S0_L003_R1_001	3,821,020	151 bp	46%		84.9%	4,571,131	160 bp	45%									3.9%	9%					6,476,526	4.1%	0%
SYN028.I0101.SG1.1_S0_L003_R2_001	3,821,020	151 bp	45%														3.8%	9%
SYN028.I0101.SG1.1_S0_L004_R1_001	3,775,264	151 bp	45%		85.0%	4,511,901	160 bp	45%									4.1%	9%					6,402,666	4.3%	0%
SYN028.I0101.SG1.1_S0_L004_R2_001	3,775,264	151 bp	46%														3.9%	9%
SYN028.I0101_L1_polyg				45.3%															1.0%	81.3%	909.4	99.9%
SYN028.I0101_L2_polyg				45.3%															1.0%	81.5%	905.3	99.8%
SYN028.I0101_L3_polyg				45.5%															1.0%	79.0%	901.2	99.9%
SYN028.I0101_L4_polyg				45.4%															1.0%	81.0%	912.0	99.8%

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)	Seqs	Total Sequences ()	`total_sequences`	read_count
\|\|	FastQC (pre-Trimming)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (pre-Trimming)	% GC	Average % GC Content	`percent_gc`	None
\|\|	fastp	GC content	GC content after filtering	`after_filtering_gc_content`	None
\|\|	Adapter Removal	% Trimmed	% trimmed reads	`percent_aligned`	percent_aligned
\|\|	FastQC (post-Trimming)	Seqs	Total Sequences ()	`total_sequences`	read_count
\|\|	FastQC (post-Trimming)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (post-Trimming)	% GC	Average % GC Content	`percent_gc`	None
\|\|	Kraken	% Unclassified	Percentage of reads that were unclassified	`% Unclassified`	None
\|\|	Samtools Flagstat (pre-samtools filter)	Reads	Total reads in the bam file ()	`flagstat_total`	read_count
\|\|	Samtools Flagstat (pre-samtools filter)	Reads Mapped	Reads Mapped in the bam file ()	`mapped_passed`	read_count
\|\|	Samtools Flagstat (post-samtools filter)	Reads	Total reads in the bam file ()	`flagstat_total`	read_count
\|\|	endorSpy	Endogenous DNA (%)	Endogenous DNA (%)	`endogenous_dna`	None
\|\|	Samtools Flagstat (post-samtools filter)	Reads Mapped	Reads Mapped in the bam file ()	`mapped_passed`	read_count
\|\|	endorSpy	Endogenous DNA Post (%)	Endogenous DNA Post (%)	`endogenous_dna_post`	None
\|\|	Picard	% Dups	Mark Duplicates - Percent Duplication	`PERCENT_DUPLICATION`	None
\|\|	FastQC (pre-Trimming)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (pre-Trimming)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	fastp	% Duplication	Duplication rate before filtering	`pct_duplication`	None
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`after_filtering_q30_rate`	None
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`after_filtering_q30_bases`	base_count
\|\|	fastp	% PF	Percent reads passing filter	`pct_surviving`	None
\|\|	Adapter Removal	Reads Trimmed	Total trimmed reads ()	`aligned_total`	read_count
\|\|	FastQC (post-Trimming)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (post-Trimming)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	Kraken	% Enterococcus faecalis	Percentage of reads that were the top Species over all samples - Enterococcus faecalis	`% Enterococcus faecalis`	None
\|\|	Kraken	% Top 5 Species	Percentage of reads that were classified by one of the top 5 Species (Enterococcus faecalis, Veillonella parvula, Enterococcus mundtii, Rothia mucilaginosa, Prevotella melaninogenica)	`% Top 5`	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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Length Distribution

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

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.

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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:

fastp

fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

Filtered Reads

Filtering statistics of sampled reads.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Duplication Rates

Duplication rates of sampled reads.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Insert Sizes

Insert size estimation of sampled reads.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Quality

Average sequencing quality over each base of all reads.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

GC Content

Average GC content over each base of all reads.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

N content

Average N content over each base of all reads.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Adapter Removal

Adapter Removal rapid adapter trimming, identification, and read merging

Retained and Discarded Paired-End Collapsed

The number of retained and discarded reads.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Length Distribution Paired End Collapsed

The length distribution of reads after processing adapter alignment.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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:

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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:

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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:

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Base Sequence Content

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

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.

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Base N Content

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

From the FastQC help:

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Length Distribution

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

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Duplication Levels

The relative level of duplication found for every sequence.

From the FastQC Help:

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.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Overrepresented sequences

The total amount of overrepresented sequences found in each library.

From the FastQC Help:

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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:

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Status Checks

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

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

Min:

Max:

Kraken

Kraken is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.

Top taxa

The number of reads falling into the top 5 taxa across different ranks.

To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top five taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

Duplication rate of top species

The duplication rate of minimizer falling into the top 5 species

To make this plot, the minimizer duplication rate is computed for the top 5 most abundant species in all samples.

The minimizer duplication rate is defined as: duplication rate = (total number of minimizers / number of distinct minimizers)

A low coverage and high duplication rate (>> 1) is often sign of read stacking, which probably indicates of false positive hit.

Min:

Max:

Samtools Flagstat (pre-samtools filter)

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools Flagstat

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

Samtools Flagstat (post-samtools filter)

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools Flagstat

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

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

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.

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.

nf-core/eager Software Versions

are collected at run time from the software output.

nf-core/eager: v2.4.1
Nextflow: v21.03.0.edge
FastQC: v0.11.9
MultiQC: v1.11
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: vVersion:2.26.0
Qualimap: v2.2.2-dev
Preseq: v3.1.1
GATK HaplotypeCaller: N/A
GATK UnifiedGenotyper: v3.5-0-g36282e4
freebayes: v1.3.5
sequenceTools: v1.4.0.5
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: v0.4.1
kraken: v2.1.2
maltextract: v1.7
eigenstrat_snp_coverage: v1.0.2
mapDamage2: v2.2.1
bbduk: vJanuary 26, 2021
bcftools: v1.12

nf-core/eager Workflow Summary

- this information is collected when the pipeline is started.

Pipeline Release: 2.4.1
Run Name: byoc_kraken
Input: /home/bartholdybp/byoc_analysis/eager/byoc_input.tsv
Fasta Ref: /home/bartholdybp/data/databases/refseq/human/GRCh38_latest_genomic.fna
Max Resources: 240 GB memory, 24 cpus, 7d time per job
Container: singularity - nfcore/eager:2.4.1
Output dir: /home/bartholdybp/data/analysis/158103//results
Launch dir: /scratchdata/bartholdybp/158103
Working dir: /home/bartholdybp/data/analysis/158103/work
Script dir: /home/bartholdybp/.nextflow/assets/nf-core/eager
User: bartholdybp
Config Profile: alice,byoc
Config Profile Description: BYOC profile for use on Leiden University ALICE cluster.
Config Profile Contact: Bjorn Peare Bartholdy (@osteobjorn)
Config Profile URL: https://wiki.alice.universiteitleiden.nl/
Config Files: /home/bartholdybp/.nextflow/assets/nf-core/eager/nextflow.config, /scratchdata/bartholdybp/158103/byoc.config

Toggle navigation v1.11

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

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

fastp

Filtered Reads

Duplication Rates

Insert Sizes

Sequence Quality

GC Content

N content

Adapter Removal

Retained and Discarded Paired-End Collapsed

Length Distribution Paired End Collapsed

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

Kraken

Top taxa Help

Duplication rate of top species Help

Samtools Flagstat (pre-samtools filter)

Samtools Flagstat

Samtools Flagstat (post-samtools filter)

Samtools Flagstat

Picard

Mark Duplicates Help

Preseq

Complexity curve

nf-core/eager Software Versions

nf-core/eager Workflow Summary

v1.11

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

Top taxa

Duplication rate of top species

Mark Duplicates