MultiQC Report

General Statistics

Showing ²⁸²/₂₈₂ rows and ²²/₂₈ columns.

Sample Name	M Reads	M Reads Mapped	% rRNA	dupInt	% Dups	5'-3' bias	M Aligned	% Proper Pairs	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs	% Aligned	M Aligned	% Dups	% GC	Length	% Failed	M Seqs	% BP Trimmed	% Dups	% GC	Length	% Failed	M Seqs
HVG3CDRXX_D128_R1	76.4	76.4	0.01%	0.04%	49.6%	1.21	18.6	21.4%	0.31%	39.2	37.2	100.0%	100.0%	7.9%	37.2	61.5%	11.8							64.5%	56%	145 bp	18%	19.2
HVG3CDRXX_D128_R1_1																		65.7%	56%	151 bp	27%	19.2	3.9%	65.4%	56%	145 bp	18%	19.2
HVG3CDRXX_D128_R1_2																		64.7%	56%	151 bp	27%	19.2	3.8%
HVG3CDRXX_D129_R1	108.1	108.1	0.00%	0.06%	47.6%	1.21	22.3	18.0%	0.33%	63.5	44.6	100.0%	100.0%	14.1%	44.6	59.6%	13.8							65.5%	58%	144 bp	18%	23.1
HVG3CDRXX_D129_R1_1																		69.2%	59%	151 bp	36%	24.8	11.0%	66.6%	58%	144 bp	18%	23.1
HVG3CDRXX_D129_R1_2																		65.9%	60%	151 bp	27%	24.8	4.4%
HVG3CDRXX_D134_R1	97.3	97.3	0.00%	0.06%	60.1%	1.14	23.3	16.6%	0.30%	50.7	46.6	100.0%	100.0%	8.1%	46.6	56.7%	13.7							72.2%	57%	144 bp	18%	24.2
HVG3CDRXX_D134_R1_1																		73.8%	57%	151 bp	27%	24.4	5.4%	73.3%	57%	144 bp	18%	24.2
HVG3CDRXX_D134_R1_2																		72.3%	57%	151 bp	27%	24.4	4.8%
HVG3CDRXX_D141_R1	76.2	76.2	0.00%	0.05%	35.6%	1.18	22.3	33.7%	0.30%	31.5	44.7	100.0%	100.0%	5.8%	44.7	73.4%	16.8							55.4%	54%	145 bp	27%	22.9
HVG3CDRXX_D141_R1_1																		58.0%	54%	151 bp	36%	23.7	7.5%	56.2%	54%	145 bp	27%	22.9
HVG3CDRXX_D141_R1_2																		56.0%	55%	151 bp	27%	23.7	4.2%
HVG3CDRXX_D161_R1	37.2	37.2	0.00%	0.05%	28.6%	1.20	11.7	40.0%	0.32%	13.8	23.4	100.0%	100.0%	4.9%	23.4	76.9%	9.3							48.8%	54%	145 bp	18%	12.0
HVG3CDRXX_D161_R1_1																		50.0%	54%	151 bp	27%	12.1	4.5%	49.5%	54%	145 bp	18%	12.0
HVG3CDRXX_D161_R1_2																		48.8%	54%	151 bp	18%	12.1	3.8%
HVG3CDRXX_D166_R1	64.5	64.5	0.00%	0.05%	41.2%	1.16	17.4	28.1%	0.29%	29.8	34.7	100.0%	100.0%	6.6%	34.7	67.9%	12.1							59.5%	56%	145 bp	18%	17.9
HVG3CDRXX_D166_R1_1																		60.8%	56%	151 bp	27%	17.9	4.3%	60.4%	56%	145 bp	18%	17.9
HVG3CDRXX_D166_R1_2																		59.6%	56%	151 bp	27%	17.9	4.0%
HVG3CDRXX_D16_R1	40.2	40.2	0.00%	0.05%	35.5%	1.21	11.2	31.5%	0.31%	17.8	22.4	100.0%	100.0%	7.1%	22.4	72.1%	8.3							54.2%	55%	146 bp	18%	11.5
HVG3CDRXX_D16_R1_1																		56.0%	55%	151 bp	36%	11.7	4.8%	55.1%	55%	146 bp	18%	11.5
HVG3CDRXX_D16_R1_2																		54.5%	55%	151 bp	27%	11.7	3.1%
HVG3CDRXX_D171_R1	83.9	83.9	0.00%	0.06%	46.0%	1.19	21.9	25.0%	0.31%	40.0	43.9	100.0%	100.0%	7.0%	43.9	66.3%	14.9							63.6%	56%	146 bp	18%	22.5
HVG3CDRXX_D171_R1_1																		65.3%	56%	151 bp	36%	22.9	4.8%	64.5%	56%	146 bp	18%	22.5
HVG3CDRXX_D171_R1_2																		63.5%	56%	151 bp	27%	22.9	3.3%
HVG3CDRXX_D184_R1	77.3	77.3	0.00%	0.05%	59.9%	1.17	17.6	15.4%	0.29%	42.2	35.1	100.0%	100.0%	9.9%	35.1	57.5%	10.4							71.9%	57%	144 bp	18%	18.1
HVG3CDRXX_D184_R1_1																		73.4%	57%	151 bp	36%	18.4	6.2%	72.7%	57%	144 bp	18%	18.1
HVG3CDRXX_D184_R1_2																		71.7%	57%	151 bp	27%	18.4	4.8%
HVG3CDRXX_D194_R1	111.7	111.7	0.00%	0.06%	58.4%	1.14	24.5	15.7%	0.27%	62.7	49.0	100.0%	100.0%	10.0%	49.0	53.5%	13.6							72.0%	58%	146 bp	27%	25.4
HVG3CDRXX_D194_R1_1																		73.7%	58%	151 bp	36%	26.0	5.8%	72.8%	58%	146 bp	27%	25.4
HVG3CDRXX_D194_R1_2																		70.8%	59%	151 bp	36%	26.0	3.5%
HVG3CDRXX_D196_R1	72.8	72.8	0.00%	0.05%	51.3%	1.21	18.3	21.3%	0.29%	36.3	36.6	100.0%	100.0%	7.8%	36.6	61.8%	11.6							66.8%	57%	145 bp	18%	18.8
HVG3CDRXX_D196_R1_1																		68.2%	57%	151 bp	27%	18.9	4.3%	67.8%	57%	145 bp	18%	18.8
HVG3CDRXX_D196_R1_2																		66.9%	57%	151 bp	27%	18.9	3.8%
HVG3CDRXX_D203_R1	111.2	111.2	0.00%	0.05%	48.1%	1.14	25.5	20.8%	0.30%	60.1	51.1	100.0%	100.0%	10.2%	51.1	61.4%	16.1							64.9%	57%	145 bp	18%	26.2
HVG3CDRXX_D203_R1_1																		66.1%	56%	151 bp	27%	26.3	4.0%	65.8%	57%	145 bp	18%	26.2
HVG3CDRXX_D203_R1_2																		65.1%	56%	151 bp	27%	26.3	3.9%
HVG3CDRXX_D224_R1	97.5	97.5	0.00%	0.05%	57.1%	1.18	23.5	18.5%	0.26%	50.5	47.0	100.0%	100.0%	7.3%	47.0	59.0%	14.3							69.8%	57%	145 bp	18%	24.2
HVG3CDRXX_D224_R1_1																		71.0%	57%	151 bp	36%	24.4	5.1%	70.5%	57%	145 bp	27%	24.2
HVG3CDRXX_D224_R1_2																		69.8%	57%	151 bp	27%	24.4	4.3%
HVG3CDRXX_D236_R1	117.1	117.1	0.00%	0.06%	56.0%	1.15	27.4	18.3%	0.29%	62.3	54.8	100.0%	100.0%	8.1%	54.8	57.7%	16.3							68.8%	57%	145 bp	27%	28.3
HVG3CDRXX_D236_R1_1																		70.8%	57%	151 bp	36%	28.8	5.5%	70.0%	57%	145 bp	27%	28.3
HVG3CDRXX_D236_R1_2																		68.4%	57%	151 bp	36%	28.8	3.7%
HVG3CDRXX_D244_R1	131.4	131.4	0.00%	0.06%	57.5%	1.21	24.7	13.0%	0.33%	82.1	49.3	100.0%	100.0%	16.3%	49.3	52.0%	13.2							72.0%	59%	142 bp	18%	25.5
HVG3CDRXX_D244_R1_1																		73.4%	58%	151 bp	27%	25.5	6.3%	73.0%	59%	142 bp	18%	25.5
HVG3CDRXX_D244_R1_2																		72.3%	58%	151 bp	27%	25.5	6.1%
HVG3CDRXX_D248_R1	81.7	81.7	0.00%	0.05%	45.5%	1.22	21.6	25.5%	0.35%	38.6	43.2	100.0%	100.0%	7.0%	43.2	65.5%	14.7							60.5%	55%	144 bp	18%	22.5
HVG3CDRXX_D248_R1_1																		64.0%	56%	151 bp	36%	23.8	10.3%	61.5%	55%	144 bp	18%	22.5
HVG3CDRXX_D248_R1_2																		61.1%	56%	151 bp	27%	23.8	4.8%
HVG3CDRXX_D263_R1	33.6	33.6	0.00%	0.06%	39.1%	1.22	8.8	27.2%	0.31%	16.0	17.6	100.0%	100.0%	7.8%	17.6	67.3%	6.1							55.6%	56%	142 bp	18%	9.1
HVG3CDRXX_D263_R1_1																		58.4%	56%	151 bp	36%	9.4	9.5%	56.3%	56%	142 bp	18%	9.1
HVG3CDRXX_D263_R1_2																		56.0%	57%	151 bp	27%	9.4	6.2%
HVG3CDRXX_D267_R1	103.1	103.1	0.00%	0.06%	55.6%	1.15	23.5	17.6%	0.31%	56.1	47.1	100.0%	100.0%	9.8%	47.1	58.0%	14.1							70.6%	58%	145 bp	18%	24.2
HVG3CDRXX_D267_R1_1																		72.5%	58%	151 bp	36%	24.9	6.4%	71.5%	58%	145 bp	18%	24.2
HVG3CDRXX_D267_R1_2																		70.6%	58%	151 bp	27%	24.9	3.8%
HVG3CDRXX_D271_R1	70.4	70.4	0.00%	0.06%	47.1%	1.17	18.3	24.5%	0.27%	33.8	36.6	100.0%	100.0%	6.5%	36.6	64.8%	12.2							62.4%	56%	143 bp	18%	18.8
HVG3CDRXX_D271_R1_1																		64.0%	56%	151 bp	27%	19.0	6.7%	63.2%	56%	143 bp	18%	18.8
HVG3CDRXX_D271_R1_2																		62.6%	56%	151 bp	27%	19.0	5.5%
HVG3CDRXX_D272_R1	58.6	58.6	0.00%	0.05%	26.1%	1.19	19.2	43.7%	0.32%	20.1	38.5	100.0%	100.0%	5.0%	38.5	80.5%	15.9							48.7%	52%	146 bp	9%	19.7
HVG3CDRXX_D272_R1_1																		52.6%	53%	151 bp	36%	20.8	8.3%	49.5%	52%	146 bp	9%	19.7
HVG3CDRXX_D272_R1_2																		48.8%	54%	151 bp	9%	20.8	3.1%
HVG3CDRXX_D283_R1	109.5	109.5	0.00%	0.06%	65.1%	1.25	19.1	9.3%	0.32%	71.2	38.3	100.0%	100.0%	19.0%	38.3	48.5%	9.6							77.5%	59%	146 bp	18%	19.8
HVG3CDRXX_D283_R1_1																		78.6%	59%	151 bp	27%	19.8	3.6%	78.3%	59%	146 bp	18%	19.8
HVG3CDRXX_D283_R1_2																		77.7%	59%	151 bp	27%	19.8	3.6%
HVG3CDRXX_D284_R1	77.2	77.2	0.00%	0.05%	43.0%	1.18	19.9	26.0%	0.30%	37.5	39.7	100.0%	100.0%	7.5%	39.7	65.9%	13.5							60.3%	55%	145 bp	18%	20.5
HVG3CDRXX_D284_R1_1																		62.0%	55%	151 bp	36%	20.8	5.2%	61.2%	55%	145 bp	18%	20.5
HVG3CDRXX_D284_R1_2																		60.2%	56%	151 bp	27%	20.8	3.8%
HVG3CDRXX_D289_R1	130.2	130.2	0.00%	0.05%	54.0%	1.22	25.6	15.1%	0.31%	79.0	51.2	100.0%	100.0%	14.9%	51.2	54.8%	14.5							70.7%	59%	147 bp	18%	26.4
HVG3CDRXX_D289_R1_1																		71.8%	58%	151 bp	18%	26.5	3.1%	71.6%	59%	147 bp	18%	26.4
HVG3CDRXX_D289_R1_2																		70.6%	58%	151 bp	18%	26.5	2.9%
HVG3CDRXX_D291_R1	105.9	105.9	0.00%	0.06%	59.6%	1.26	23.5	15.4%	0.28%	58.9	46.9	100.0%	99.9%	9.6%	46.9	54.5%	13.3							73.2%	59%	147 bp	18%	24.4
HVG3CDRXX_D291_R1_1																		74.5%	58%	151 bp	18%	24.6	3.6%	74.2%	59%	147 bp	18%	24.4
HVG3CDRXX_D291_R1_2																		73.0%	59%	151 bp	18%	24.6	2.9%
HVG3CDRXX_D292_R1	109.2	109.2	0.00%	0.06%	77.1%	1.15	23.4	8.3%	0.24%	62.4	46.8	100.0%	100.0%	6.6%	46.8	42.9%	10.4							83.8%	60%	147 bp	27%	24.3
HVG3CDRXX_D292_R1_1																		84.9%	60%	151 bp	27%	24.5	3.3%	84.7%	60%	147 bp	27%	24.3
HVG3CDRXX_D292_R1_2																		83.6%	60%	151 bp	27%	24.5	2.7%
HVG3CDRXX_D293_R1	116.5	116.5	0.00%	0.05%	54.1%	1.27	22.9	14.8%	0.34%	70.6	45.9	100.0%	100.0%	14.7%	45.9	54.0%	12.9							68.2%	58%	144 bp	18%	23.9
HVG3CDRXX_D293_R1_1																		72.1%	59%	151 bp	36%	26.1	12.9%	69.1%	58%	144 bp	18%	23.9
HVG3CDRXX_D293_R1_2																		68.3%	60%	151 bp	36%	26.1	4.7%
HVG3CDRXX_D299_R1	62.6	62.6	0.00%	0.06%	46.0%	1.18	17.0	26.3%	0.33%	28.5	34.1	100.0%	100.0%	5.6%	34.1	66.3%	11.8							60.5%	55%	145 bp	18%	17.7
HVG3CDRXX_D299_R1_1																		66.1%	57%	151 bp	45%	19.9	14.2%	61.7%	55%	145 bp	18%	17.7
HVG3CDRXX_D299_R1_2																		61.4%	59%	151 bp	36%	19.9	3.5%
HVG3CDRXX_D303_R1	100.1	100.1	0.00%	0.05%	64.5%	1.26	21.1	12.6%	0.27%	57.8	42.3	100.0%	100.0%	10.1%	42.3	49.1%	10.7							76.5%	59%	146 bp	18%	21.9
HVG3CDRXX_D303_R1_1																		77.8%	59%	151 bp	36%	22.3	4.8%	77.2%	59%	146 bp	27%	21.9
HVG3CDRXX_D303_R1_2																		76.1%	60%	151 bp	27%	22.3	3.1%
HVG3CDRXX_D305_R1	20.2	20.2	0.00%	0.07%	33.3%	1.19	4.7	25.3%	0.33%	10.8	9.5	100.0%	100.0%	12.0%	9.5	66.8%	3.2							49.0%	55%	142 bp	9%	4.9
HVG3CDRXX_D305_R1_1																		51.0%	55%	151 bp	27%	4.9	6.9%	49.9%	55%	142 bp	9%	4.9
HVG3CDRXX_D305_R1_2																		49.1%	56%	151 bp	18%	4.9	5.9%
HVG3CDRXX_D306_R1	119.9	119.9	0.00%	0.06%	59.8%	1.20	26.2	15.1%	0.29%	67.4	52.5	100.0%	100.0%	9.8%	52.5	54.3%	14.7							72.6%	59%	145 bp	18%	27.0
HVG3CDRXX_D306_R1_1																		74.8%	59%	151 bp	36%	27.7	6.0%	74.0%	59%	145 bp	27%	27.0
HVG3CDRXX_D306_R1_2																		72.5%	59%	151 bp	27%	27.7	3.7%
HVG3CDRXX_D307_R1	79.9	79.9	0.00%	0.05%	59.0%	1.20	18.9	16.8%	0.29%	42.0	37.9	100.0%	100.0%	7.5%	37.9	56.1%	11.0							70.8%	57%	146 bp	18%	19.6
HVG3CDRXX_D307_R1_1																		71.8%	57%	151 bp	27%	19.7	3.4%	71.6%	57%	146 bp	18%	19.6
HVG3CDRXX_D307_R1_2																		70.9%	57%	151 bp	27%	19.7	3.3%
HVG3CDRXX_D308_R1	58.8	58.8	0.00%	0.07%	72.5%	1.29	12.6	9.9%	0.29%	33.6	25.2	100.0%	99.9%	8.8%	25.2	46.2%	6.1							79.4%	58%	146 bp	27%	13.2
HVG3CDRXX_D308_R1_1																		80.7%	58%	151 bp	36%	13.4	4.1%	80.4%	58%	146 bp	27%	13.2
HVG3CDRXX_D308_R1_2																		79.1%	58%	151 bp	36%	13.4	3.4%
HVG3CDRXX_D309_R1	95.6	95.6	0.00%	0.06%	67.1%	1.25	21.2	12.7%	0.26%	53.2	42.5	100.0%	100.0%	8.0%	42.5	50.8%	11.1							76.8%	58%	146 bp	27%	21.9
HVG3CDRXX_D309_R1_1																		79.2%	59%	151 bp	36%	23.4	9.3%	77.7%	58%	146 bp	27%	21.9
HVG3CDRXX_D309_R1_2																		76.2%	60%	151 bp	36%	23.4	3.2%
HVG3CDRXX_D30_R1	79.3	79.3	0.00%	0.06%	47.1%	1.22	19.9	23.2%	0.30%	39.5	39.8	100.0%	100.0%	8.4%	39.8	64.6%	13.3							63.7%	56%	145 bp	18%	20.5
HVG3CDRXX_D30_R1_1																		65.0%	56%	151 bp	27%	20.7	4.9%	64.5%	56%	145 bp	18%	20.5
HVG3CDRXX_D30_R1_2																		63.7%	56%	151 bp	27%	20.7	4.3%
HVG3CDRXX_D310_R1	61.7	61.7	0.00%	0.05%	58.2%	1.14	14.5	17.1%	0.28%	32.6	29.0	100.0%	99.9%	7.6%	29.0	55.0%	8.3							68.5%	57%	146 bp	18%	15.0
HVG3CDRXX_D310_R1_1																		70.5%	58%	151 bp	36%	15.6	7.0%	69.2%	57%	146 bp	27%	15.0
HVG3CDRXX_D310_R1_2																		68.4%	58%	151 bp	27%	15.6	3.4%
HVG3CDRXX_D312_R1	99.2	99.2	0.00%	0.05%	51.5%	1.16	25.4	22.1%	0.28%	48.4	50.8	100.0%	100.0%	6.9%	50.8	63.3%	16.5							66.8%	56%	146 bp	18%	26.0
HVG3CDRXX_D312_R1_1																		68.4%	56%	151 bp	36%	26.4	4.3%	67.8%	56%	146 bp	18%	26.0
HVG3CDRXX_D312_R1_2																		66.7%	57%	151 bp	27%	26.4	3.1%
HVG3CDRXX_D315_R1	64.5	64.5	0.00%	0.05%	48.1%	1.15	16.4	23.3%	0.30%	31.8	32.7	100.0%	100.0%	6.4%	32.7	61.9%	10.5							61.3%	56%	145 bp	18%	16.9
HVG3CDRXX_D315_R1_1																		64.1%	57%	151 bp	36%	17.7	8.2%	62.3%	56%	145 bp	27%	16.9
HVG3CDRXX_D315_R1_2																		60.7%	57%	151 bp	27%	17.7	4.1%
HVG3CDRXX_D316_R1	0.0	0.0	0.00%	0.00%	1.8%	1.34	0.0	33.9%	0.40%	0.0	0.0	100.0%	99.9%	8.9%	0.0	61.9%	0.0							14.7%	52%	142 bp	36%	0.0
HVG3CDRXX_D316_R1_1																		19.6%	53%	151 bp	36%	0.0	10.9%	16.0%	52%	142 bp	36%	0.0
HVG3CDRXX_D316_R1_2																		14.2%	53%	151 bp	36%	0.0	6.0%
HVG3CDRXX_D320_R1	89.3	89.3	0.00%	0.06%	53.6%	1.19	20.8	18.5%	0.31%	47.7	41.6	100.0%	100.0%	9.4%	41.6	59.3%	12.8							67.6%	56%	144 bp	18%	21.6
HVG3CDRXX_D320_R1_1																		69.0%	56%	151 bp	27%	21.7	4.5%	68.6%	56%	144 bp	18%	21.6
HVG3CDRXX_D320_R1_2																		67.8%	56%	151 bp	27%	21.7	4.4%
HVG3CDRXX_D322_R1	106.6	106.6	0.00%	0.05%	66.7%	1.19	24.3	13.3%	0.27%	58.0	48.6	100.0%	100.0%	8.9%	48.6	55.0%	13.7							77.0%	57%	147 bp	18%	25.0
HVG3CDRXX_D322_R1_1																		78.3%	57%	151 bp	27%	25.3	4.2%	77.9%	57%	147 bp	27%	25.0
HVG3CDRXX_D322_R1_2																		76.6%	58%	151 bp	18%	25.3	2.8%
HVG3CDRXX_D323_R1	83.9	83.9	0.00%	0.05%	66.2%	1.19	18.3	12.4%	0.28%	47.2	36.7	100.0%	100.0%	8.8%	36.7	50.0%	9.5							76.9%	59%	147 bp	27%	19.0
HVG3CDRXX_D323_R1_1																		78.4%	59%	151 bp	27%	19.4	4.9%	77.8%	59%	147 bp	27%	19.0
HVG3CDRXX_D323_R1_2																		76.0%	59%	151 bp	27%	19.4	2.9%
HVG3CDRXX_D328_R1	96.4	96.4	0.00%	0.06%	40.0%	1.22	28.2	31.3%	0.31%	40.0	56.5	100.0%	100.0%	5.8%	56.5	71.8%	20.9							61.0%	55%	146 bp	18%	29.1
HVG3CDRXX_D328_R1_1																		64.5%	56%	151 bp	36%	30.9	9.2%	62.0%	55%	146 bp	18%	29.1
HVG3CDRXX_D328_R1_2																		62.4%	57%	151 bp	36%	30.9	3.6%
HVG3CDRXX_D330_R1	82.3	82.3	0.00%	0.05%	55.8%	1.23	18.7	16.8%	0.32%	44.9	37.4	100.0%	100.0%	10.6%	37.4	59.5%	11.5							70.6%	57%	147 bp	18%	19.3
HVG3CDRXX_D330_R1_1																		71.6%	57%	151 bp	18%	19.3	2.5%	71.4%	57%	147 bp	18%	19.3
HVG3CDRXX_D330_R1_2																		70.6%	57%	151 bp	18%	19.3	2.5%
HVG3CDRXX_D333_R1	123.2	123.2	0.00%	0.06%	65.9%	1.18	23.1	10.1%	0.32%	77.0	46.2	100.0%	100.0%	15.4%	46.2	47.6%	11.4							77.6%	59%	145 bp	18%	24.1
HVG3CDRXX_D333_R1_1																		79.2%	59%	151 bp	36%	24.1	3.8%	79.0%	59%	145 bp	27%	24.1
HVG3CDRXX_D333_R1_2																		77.7%	59%	151 bp	27%	24.1	3.7%
HVG3CDRXX_D338_R1	117.2	117.2	0.00%	0.05%	73.1%	1.24	24.2	9.2%	0.26%	68.9	48.4	100.0%	100.0%	9.7%	48.4	46.6%	11.6							81.9%	60%	148 bp	27%	25.0
HVG3CDRXX_D338_R1_1																		83.2%	60%	151 bp	27%	25.0	2.3%	83.1%	60%	148 bp	27%	25.0
HVG3CDRXX_D338_R1_2																		81.9%	60%	151 bp	27%	25.0	2.3%
HVG3CDRXX_D340_R1	87.0	87.0	0.00%	0.07%	32.1%	1.20	23.4	32.0%	0.34%	40.3	46.8	100.0%	100.0%	9.7%	46.8	76.7%	18.4							56.1%	52%	147 bp	18%	24.0
HVG3CDRXX_D340_R1_1																		57.4%	52%	151 bp	27%	24.0	3.0%	57.1%	52%	147 bp	18%	24.0
HVG3CDRXX_D340_R1_2																		56.2%	52%	151 bp	18%	24.0	3.0%
HVG3CDRXX_D341_R1	117.9	117.9	0.00%	0.06%	80.2%	1.18	23.9	6.9%	0.22%	70.2	47.8	100.0%	100.0%	7.9%	47.8	42.6%	10.5							86.4%	60%	148 bp	27%	24.5
HVG3CDRXX_D341_R1_1																		87.3%	60%	151 bp	27%	24.6	2.0%	87.2%	60%	148 bp	27%	24.5
HVG3CDRXX_D341_R1_2																		86.3%	60%	151 bp	27%	24.6	1.9%
HVG3CDRXX_D342_R1	101.9	101.9	0.00%	0.07%	47.5%	1.17	24.9	22.7%	0.28%	52.1	49.8	100.0%	100.0%	8.4%	49.8	64.3%	16.4							64.9%	57%	146 bp	18%	25.5
HVG3CDRXX_D342_R1_1																		65.9%	57%	151 bp	27%	25.5	3.3%	65.8%	57%	146 bp	18%	25.5
HVG3CDRXX_D342_R1_2																		64.9%	57%	151 bp	27%	25.5	3.2%
HVG3CDRXX_D343_R1	77.6	77.6	0.00%	0.04%	50.1%	1.18	20.0	23.1%	0.29%	37.5	40.0	100.0%	100.0%	6.0%	40.0	62.8%	13.0							64.9%	56%	147 bp	18%	20.6
HVG3CDRXX_D343_R1_1																		66.8%	56%	151 bp	27%	20.9	4.2%	66.2%	56%	147 bp	27%	20.6
HVG3CDRXX_D343_R1_2																		64.7%	57%	151 bp	18%	20.9	2.8%
HVG3CDRXX_D344_R1	98.0	98.0	0.00%	0.05%	60.7%	1.22	20.1	13.4%	0.30%	57.7	40.3	100.0%	100.0%	12.1%	40.3	51.4%	10.7							73.8%	59%	146 bp	18%	20.8
HVG3CDRXX_D344_R1_1																		75.1%	59%	151 bp	36%	20.9	3.4%	74.9%	59%	146 bp	27%	20.8
HVG3CDRXX_D344_R1_2																		73.8%	59%	151 bp	27%	20.9	3.2%
HVG3CDRXX_D345_R1	107.8	107.8	0.00%	0.07%	43.7%	1.21	28.2	25.9%	0.31%	51.4	56.4	100.0%	100.0%	7.7%	56.4	68.2%	19.9							63.4%	56%	147 bp	18%	29.1
HVG3CDRXX_D345_R1_1																		64.9%	56%	151 bp	18%	29.3	3.0%	64.6%	56%	147 bp	18%	29.1
HVG3CDRXX_D345_R1_2																		63.4%	56%	151 bp	18%	29.3	2.7%
HVG3CDRXX_D347_R1	99.2	99.2	0.00%	0.06%	59.7%	1.20	22.7	16.0%	0.28%	53.8	45.4	100.0%	100.0%	8.7%	45.4	55.2%	13.0							72.9%	58%	146 bp	18%	23.6
HVG3CDRXX_D347_R1_1																		75.3%	59%	151 bp	36%	24.4	6.9%	74.2%	58%	146 bp	27%	23.6
HVG3CDRXX_D347_R1_2																		72.8%	59%	151 bp	27%	24.4	3.4%
HVG3CDRXX_D348_R1	74.4	74.4	0.00%	0.05%	46.7%	1.20	19.8	25.0%	0.29%	34.8	39.6	100.0%	100.0%	7.0%	39.6	67.1%	13.7							63.7%	55%	147 bp	18%	20.4
HVG3CDRXX_D348_R1_1																		64.9%	55%	151 bp	18%	20.4	2.7%	64.8%	56%	147 bp	18%	20.4
HVG3CDRXX_D348_R1_2																		63.7%	55%	151 bp	18%	20.4	2.7%
HVG3CDRXX_D349_R1	91.0	91.0	0.00%	0.05%	54.8%	1.22	21.8	18.8%	0.30%	47.3	43.7	100.0%	100.0%	8.2%	43.7	60.4%	13.6							70.0%	57%	147 bp	18%	22.6
HVG3CDRXX_D349_R1_1																		71.1%	57%	151 bp	27%	22.6	3.1%	71.0%	57%	147 bp	18%	22.6
HVG3CDRXX_D349_R1_2																		70.0%	57%	151 bp	27%	22.6	3.0%
HVG3CDRXX_D350_R1	58.8	58.8	0.00%	0.05%	37.8%	1.16	15.3	28.5%	0.31%	28.1	30.7	100.0%	100.0%	7.5%	30.7	66.5%	10.6							56.9%	55%	146 bp	18%	16.0
HVG3CDRXX_D350_R1_1																		58.1%	55%	151 bp	36%	16.1	3.8%	57.8%	55%	146 bp	27%	16.0
HVG3CDRXX_D350_R1_2																		56.9%	55%	151 bp	27%	16.1	3.4%
HVG3CDRXX_D353_R1	93.7	93.7	0.00%	0.05%	55.7%	1.20	22.7	18.6%	0.27%	48.3	45.3	100.0%	100.0%	8.4%	45.3	59.9%	14.0							70.6%	57%	147 bp	18%	23.4
HVG3CDRXX_D353_R1_1																		72.0%	57%	151 bp	36%	23.8	4.6%	71.4%	57%	147 bp	18%	23.4
HVG3CDRXX_D353_R1_2																		70.3%	57%	151 bp	27%	23.8	3.0%
HVG3CDRXX_D356_R1	84.7	84.7	0.00%	0.05%	58.9%	1.25	18.3	14.9%	0.29%	48.1	36.6	100.0%	100.0%	10.9%	36.6	54.9%	10.4							72.7%	58%	146 bp	18%	18.9
HVG3CDRXX_D356_R1_1																		73.9%	58%	151 bp	27%	18.9	3.4%	73.7%	58%	146 bp	18%	18.9
HVG3CDRXX_D356_R1_2																		72.8%	58%	151 bp	27%	18.9	3.3%
HVG3CDRXX_D357_R1	73.3	73.3	0.00%	0.04%	54.7%	1.21	17.8	19.1%	0.29%	37.7	35.6	100.0%	100.0%	7.4%	35.6	59.8%	11.0							69.1%	57%	147 bp	18%	18.3
HVG3CDRXX_D357_R1_1																		70.7%	57%	151 bp	18%	18.6	3.6%	70.3%	57%	147 bp	18%	18.3
HVG3CDRXX_D357_R1_2																		68.8%	57%	151 bp	18%	18.6	2.5%
HVG3CDRXX_D358_R1	182.1	182.1	0.00%	0.06%	73.0%	1.22	37.3	9.3%	0.31%	107.4	74.7	100.0%	100.0%	10.4%	74.7	45.6%	17.8							81.7%	60%	146 bp	27%	39.1
HVG3CDRXX_D358_R1_1																		83.4%	59%	151 bp	36%	39.4	4.0%	83.2%	60%	146 bp	27%	39.1
HVG3CDRXX_D358_R1_2																		81.6%	60%	151 bp	36%	39.4	3.4%
HVG3CDRXX_D359_R1	93.0	93.0	0.01%	0.06%	66.3%	1.27	21.2	13.0%	0.28%	50.6	42.4	100.0%	100.0%	8.2%	42.4	52.4%	11.5							77.2%	59%	145 bp	18%	21.9
HVG3CDRXX_D359_R1_1																		78.9%	59%	151 bp	36%	22.4	5.9%	78.2%	59%	145 bp	27%	21.9
HVG3CDRXX_D359_R1_2																		76.5%	59%	151 bp	27%	22.4	3.9%
HVG3CDRXX_D362_R1	61.0	61.0	0.00%	0.06%	63.8%	1.20	13.5	13.9%	0.27%	33.9	27.0	100.0%	100.0%	8.5%	27.0	50.9%	7.1							73.6%	58%	146 bp	27%	14.0
HVG3CDRXX_D362_R1_1																		74.5%	58%	151 bp	36%	14.1	3.6%	74.3%	58%	146 bp	27%	14.0
HVG3CDRXX_D362_R1_2																		73.5%	58%	151 bp	36%	14.1	3.4%
HVG3CDRXX_D363_R1	70.7	70.7	0.00%	0.05%	51.7%	1.20	18.7	22.6%	0.27%	33.4	37.4	100.0%	100.0%	5.7%	37.4	62.9%	12.1							67.3%	56%	147 bp	18%	19.3
HVG3CDRXX_D363_R1_1																		68.7%	57%	151 bp	27%	19.8	5.2%	67.8%	56%	147 bp	18%	19.3
HVG3CDRXX_D363_R1_2																		66.8%	57%	151 bp	18%	19.8	2.9%
HVG3CDRXX_D364_R1	97.7	97.7	0.00%	0.06%	59.9%	1.15	21.3	15.1%	0.28%	55.1	42.6	100.0%	100.0%	10.7%	42.6	54.9%	12.0							72.5%	57%	147 bp	27%	21.9
HVG3CDRXX_D364_R1_1																		73.5%	57%	151 bp	27%	22.0	2.9%	73.4%	57%	147 bp	27%	21.9
HVG3CDRXX_D364_R1_2																		72.5%	57%	151 bp	27%	22.0	2.7%
HVG3CDRXX_D376_R1	86.7	86.7	0.00%	0.06%	72.5%	1.20	18.5	10.2%	0.25%	49.5	37.1	100.0%	100.0%	8.9%	37.1	46.0%	8.9							80.2%	59%	145 bp	27%	19.4
HVG3CDRXX_D376_R1_1																		81.2%	59%	151 bp	36%	19.4	4.2%	81.1%	59%	145 bp	27%	19.4
HVG3CDRXX_D376_R1_2																		80.1%	59%	151 bp	36%	19.4	4.0%
HVG3CDRXX_D382_R1	90.8	90.8	0.00%	0.06%	62.6%	1.19	21.0	15.1%	0.25%	48.8	42.0	100.0%	100.0%	8.4%	42.0	54.8%	11.9							74.4%	58%	146 bp	27%	21.7
HVG3CDRXX_D382_R1_1																		75.6%	58%	151 bp	36%	21.9	3.7%	75.3%	58%	147 bp	27%	21.7
HVG3CDRXX_D382_R1_2																		74.3%	58%	151 bp	36%	21.9	3.1%
HVG3CDRXX_D397_R1	83.8	83.8	0.00%	0.05%	60.5%	1.21	20.2	16.7%	0.29%	43.4	40.4	100.0%	100.0%	7.2%	40.4	56.1%	11.7							72.4%	58%	148 bp	18%	20.8
HVG3CDRXX_D397_R1_1																		73.7%	58%	151 bp	18%	20.9	2.1%	73.6%	58%	148 bp	18%	20.8
HVG3CDRXX_D397_R1_2																		72.4%	58%	151 bp	18%	20.9	2.1%
HVG3CDRXX_D401_R1	67.5	67.5	0.00%	0.05%	34.5%	1.18	19.0	32.5%	0.32%	29.6	37.9	100.0%	100.0%	7.5%	37.9	74.0%	14.4							55.1%	54%	147 bp	18%	19.4
HVG3CDRXX_D401_R1_1																		56.1%	54%	151 bp	27%	19.5	2.9%	56.0%	54%	147 bp	18%	19.4
HVG3CDRXX_D401_R1_2																		55.2%	54%	151 bp	27%	19.5	2.9%
HVG3CDRXX_D420_R1	72.2	72.2	0.00%	0.05%	40.8%	1.16	20.0	29.4%	0.33%	32.1	40.1	100.0%	100.0%	5.8%	40.1	69.4%	14.3							58.2%	55%	147 bp	18%	20.7
HVG3CDRXX_D420_R1_1																		60.5%	55%	151 bp	27%	21.1	5.0%	59.4%	55%	147 bp	18%	20.7
HVG3CDRXX_D420_R1_2																		58.3%	55%	151 bp	18%	21.1	2.9%
HVG3CDRXX_D421_R1	104.2	104.2	0.00%	0.07%	51.3%	1.25	27.1	22.5%	0.30%	50.0	54.2	100.0%	100.0%	6.6%	54.2	64.1%	17.8							67.7%	56%	147 bp	18%	27.8
HVG3CDRXX_D421_R1_1																		68.8%	56%	151 bp	18%	27.8	2.6%	68.6%	56%	147 bp	18%	27.8
HVG3CDRXX_D421_R1_2																		67.7%	56%	151 bp	18%	27.8	2.5%
HVG3CDRXX_D430_R1	116.5	116.5	0.00%	0.06%	50.9%	1.17	24.4	17.3%	0.34%	67.7	48.8	100.0%	100.0%	14.1%	48.8	60.1%	15.2							67.2%	57%	145 bp	18%	25.2
HVG3CDRXX_D430_R1_1																		68.4%	56%	151 bp	27%	25.3	4.1%	68.1%	57%	145 bp	18%	25.2
HVG3CDRXX_D430_R1_2																		67.3%	56%	151 bp	27%	25.3	4.0%
HVG3CDRXX_D439_R1	82.8	82.8	0.00%	0.06%	49.4%	1.21	22.6	24.4%	0.31%	37.6	45.2	100.0%	100.0%	6.1%	45.2	67.0%	15.6							63.5%	55%	145 bp	18%	23.3
HVG3CDRXX_D439_R1_1																		66.6%	56%	151 bp	36%	24.7	9.6%	64.4%	55%	145 bp	18%	23.3
HVG3CDRXX_D439_R1_2																		63.4%	57%	151 bp	27%	24.7	4.2%
HVG3CDRXX_D440_R1	104.7	104.7	0.00%	0.05%	57.8%	1.16	22.2	14.9%	0.32%	60.4	44.3	100.0%	100.0%	12.1%	44.3	55.0%	12.7							71.3%	58%	146 bp	18%	23.0
HVG3CDRXX_D440_R1_1																		72.6%	58%	151 bp	27%	23.1	3.7%	72.3%	58%	146 bp	18%	23.0
HVG3CDRXX_D440_R1_2																		71.1%	58%	151 bp	27%	23.1	3.3%
HVG3CDRXX_D445_R1	94.8	94.8	0.00%	0.05%	54.9%	1.26	24.0	20.3%	0.29%	46.8	47.9	100.0%	100.0%	6.5%	47.9	61.7%	15.2							70.0%	57%	148 bp	18%	24.6
HVG3CDRXX_D445_R1_1																		71.3%	57%	151 bp	18%	24.9	2.9%	71.0%	57%	148 bp	18%	24.6
HVG3CDRXX_D445_R1_2																		69.7%	57%	151 bp	18%	24.9	1.9%
HVG3CDRXX_D453_R1	126.5	126.5	0.00%	0.05%	72.1%	1.19	24.5	8.5%	0.30%	77.5	49.0	100.0%	99.9%	12.2%	49.0	46.4%	11.8							81.4%	59%	148 bp	18%	25.4
HVG3CDRXX_D453_R1_1																		82.5%	59%	151 bp	18%	25.5	2.8%	82.3%	59%	148 bp	18%	25.4
HVG3CDRXX_D453_R1_2																		81.2%	59%	151 bp	18%	25.5	2.4%
HVG3CDRXX_D454_R1	61.7	61.7	0.00%	0.05%	65.0%	1.20	11.8	10.5%	0.29%	38.0	23.7	100.0%	100.0%	15.1%	23.7	47.9%	5.9							75.7%	60%	146 bp	18%	12.2
HVG3CDRXX_D454_R1_1																		77.2%	60%	151 bp	36%	12.4	4.4%	76.8%	60%	146 bp	27%	12.2
HVG3CDRXX_D454_R1_2																		75.5%	60%	151 bp	27%	12.4	3.3%
HVG3CDRXX_D460_R1	116.0	116.0	0.00%	0.05%	69.7%	1.21	24.3	10.6%	0.30%	67.3	48.7	100.0%	100.0%	10.6%	48.7	49.2%	12.4							79.5%	59%	146 bp	18%	25.3
HVG3CDRXX_D460_R1_1																		80.8%	59%	151 bp	27%	25.5	3.8%	80.5%	59%	146 bp	18%	25.3
HVG3CDRXX_D460_R1_2																		79.1%	59%	151 bp	27%	25.5	3.1%
HVG3CDRXX_D467_R1	89.2	89.2	0.00%	0.05%	50.4%	1.19	22.0	21.5%	0.31%	45.2	44.0	100.0%	99.9%	6.9%	44.0	60.2%	13.7							66.2%	57%	145 bp	18%	22.8
HVG3CDRXX_D467_R1_1																		68.9%	58%	151 bp	36%	23.8	8.1%	67.2%	57%	145 bp	18%	22.8
HVG3CDRXX_D467_R1_2																		66.3%	59%	151 bp	27%	23.8	4.0%
HVG3CDRXX_D469_R1	91.1	91.1	0.00%	0.06%	62.1%	1.25	20.4	14.7%	0.27%	50.2	40.9	100.0%	100.0%	8.9%	40.9	53.0%	11.2							75.1%	59%	147 bp	27%	21.1
HVG3CDRXX_D469_R1_1																		76.8%	59%	151 bp	27%	21.6	5.0%	76.1%	59%	147 bp	27%	21.1
HVG3CDRXX_D469_R1_2																		75.0%	60%	151 bp	27%	21.6	2.8%
HVG3CDRXX_D473_R1	62.9	62.9	0.00%	0.05%	40.5%	1.20	15.8	26.0%	0.32%	31.2	31.7	100.0%	100.0%	9.1%	31.7	66.8%	10.9							58.2%	55%	145 bp	18%	16.4
HVG3CDRXX_D473_R1_1																		60.0%	55%	151 bp	27%	16.7	5.8%	59.1%	55%	145 bp	18%	16.4
HVG3CDRXX_D473_R1_2																		58.6%	56%	151 bp	27%	16.7	4.3%
HVG3CDRXX_D477_R1	97.0	97.0	0.00%	0.05%	38.6%	1.19	21.3	22.8%	0.37%	54.5	42.5	100.0%	100.0%	14.0%	42.5	66.0%	14.5							60.1%	57%	146 bp	18%	21.9
HVG3CDRXX_D477_R1_1																		62.4%	57%	151 bp	36%	22.5	5.4%	61.2%	57%	146 bp	18%	21.9
HVG3CDRXX_D477_R1_2																		59.4%	57%	151 bp	27%	22.5	3.0%
HVG3CDRXX_D481_R1	100.9	100.9	0.00%	0.05%	62.4%	1.17	22.5	14.5%	0.29%	56.0	45.0	100.0%	100.0%	8.2%	45.0	53.8%	12.5							73.6%	58%	144 bp	27%	23.2
HVG3CDRXX_D481_R1_1																		74.9%	58%	151 bp	36%	23.4	5.1%	74.5%	58%	144 bp	27%	23.2
HVG3CDRXX_D481_R1_2																		73.6%	58%	151 bp	36%	23.4	4.7%
HVG3CDRXX_D482_R1	103.2	103.2	0.00%	0.05%	65.9%	1.23	21.0	11.5%	0.28%	61.1	42.1	100.0%	100.0%	11.1%	42.1	49.4%	10.8							76.5%	59%	145 bp	27%	21.8
HVG3CDRXX_D482_R1_1																		78.3%	59%	151 bp	36%	22.4	6.6%	77.5%	59%	145 bp	27%	21.8
HVG3CDRXX_D482_R1_2																		76.5%	59%	151 bp	36%	22.4	4.0%
HVG3CDRXX_D487_R1	56.3	56.3	0.00%	0.06%	23.6%	1.22	19.6	48.5%	0.35%	17.1	39.2	100.0%	100.0%	3.6%	39.2	82.2%	16.5							48.4%	53%	147 bp	18%	20.1
HVG3CDRXX_D487_R1_1																		49.5%	52%	151 bp	18%	20.1	2.8%	49.4%	53%	147 bp	18%	20.1
HVG3CDRXX_D487_R1_2																		48.4%	53%	151 bp	18%	20.1	2.7%
HVG3CDRXX_D488_R1	62.0	62.0	0.00%	0.06%	34.4%	1.18	14.1	25.3%	0.39%	33.6	28.3	100.0%	100.0%	12.4%	28.3	66.2%	9.8							53.2%	56%	146 bp	18%	14.8
HVG3CDRXX_D488_R1_1																		60.6%	58%	151 bp	36%	16.9	15.5%	54.4%	56%	146 bp	18%	14.8
HVG3CDRXX_D488_R1_2																		54.0%	59%	151 bp	27%	16.9	3.2%
HVG3CDRXX_D495_R1	86.9	86.9	0.00%	0.05%	47.1%	1.20	21.8	23.5%	0.31%	43.2	43.7	100.0%	100.0%	7.9%	43.7	65.0%	14.6							64.3%	55%	147 bp	18%	22.5
HVG3CDRXX_D495_R1_1																		65.3%	55%	151 bp	18%	22.5	2.8%	65.2%	55%	147 bp	18%	22.5
HVG3CDRXX_D495_R1_2																		64.4%	55%	151 bp	18%	22.5	2.8%
HVG3CDRXX_D497_R1	64.9	64.9	0.00%	0.06%	45.6%	1.22	17.2	25.7%	0.33%	30.5	34.3	100.0%	100.0%	6.7%	34.3	65.4%	11.6							62.1%	56%	148 bp	18%	17.8
HVG3CDRXX_D497_R1_1																		64.8%	57%	151 bp	18%	18.2	4.2%	63.8%	56%	149 bp	18%	17.8
HVG3CDRXX_D497_R1_2																		62.4%	57%	151 bp	18%	18.2	1.7%
HVG3CDRXX_D498_R1	98.5	98.5	0.00%	0.05%	53.1%	1.21	23.3	19.0%	0.33%	51.9	46.6	100.0%	100.0%	9.5%	46.6	61.1%	14.7							68.6%	57%	145 bp	18%	24.1
HVG3CDRXX_D498_R1_1																		70.5%	56%	151 bp	27%	24.3	4.3%	70.1%	57%	145 bp	18%	24.1
HVG3CDRXX_D498_R1_2																		68.7%	57%	151 bp	27%	24.3	3.8%
HVG3CDRXX_D501_R1	70.4	70.4	0.00%	0.06%	51.4%	1.23	17.4	20.4%	0.36%	35.7	34.7	100.0%	100.0%	8.8%	34.7	62.8%	11.3							64.7%	57%	145 bp	18%	17.9
HVG3CDRXX_D501_R1_1																		67.4%	57%	151 bp	27%	18.1	5.1%	66.8%	57%	145 bp	18%	17.9
HVG3CDRXX_D501_R1_2																		64.7%	57%	151 bp	27%	18.1	4.2%
HVG3CDRXX_D504_R1	103.9	103.9	0.00%	0.05%	50.1%	1.20	23.8	19.8%	0.33%	56.3	47.6	100.0%	100.0%	10.1%	47.6	60.2%	14.8							66.5%	57%	147 bp	18%	24.6
HVG3CDRXX_D504_R1_1																		68.4%	57%	151 bp	27%	24.7	3.3%	68.1%	57%	147 bp	18%	24.6
HVG3CDRXX_D504_R1_2																		66.4%	57%	151 bp	18%	24.7	2.9%
HVG3CDRXX_D510_R1	92.7	92.7	0.00%	0.07%	47.7%	1.22	23.8	23.8%	0.30%	45.2	47.5	100.0%	100.0%	7.3%	47.5	65.0%	15.9							66.1%	57%	147 bp	18%	24.5
HVG3CDRXX_D510_R1_1																		67.7%	57%	151 bp	36%	24.9	4.3%	67.1%	57%	147 bp	18%	24.5
HVG3CDRXX_D510_R1_2																		66.0%	57%	151 bp	27%	24.9	2.9%
HVG3CDRXX_D65_R1	79.9	79.9	0.00%	0.05%	49.8%	1.15	17.1	18.1%	0.30%	45.7	34.2	100.0%	100.0%	12.5%	34.2	57.6%	10.1							66.2%	57%	146 bp	18%	17.6
HVG3CDRXX_D65_R1_1																		68.7%	58%	151 bp	36%	18.2	6.6%	67.4%	57%	146 bp	27%	17.6
HVG3CDRXX_D65_R1_2																		65.6%	58%	151 bp	27%	18.2	3.3%
HVG3CDRXX_D66_R1	60.7	60.7	0.00%	0.05%	39.3%	1.16	17.9	32.5%	0.30%	24.9	35.8	100.0%	100.0%	4.7%	35.8	71.2%	13.1							56.7%	54%	144 bp	18%	18.4
HVG3CDRXX_D66_R1_1																		57.9%	54%	151 bp	27%	18.4	4.8%	57.6%	55%	144 bp	18%	18.4
HVG3CDRXX_D66_R1_2																		56.8%	54%	151 bp	27%	18.4	4.5%
HVG3CDRXX_D83_R1	92.1	92.1	0.00%	0.05%	51.2%	1.13	23.8	22.8%	0.31%	44.5	47.6	100.0%	100.0%	6.1%	47.6	62.5%	15.3							65.4%	56%	144 bp	18%	24.5
HVG3CDRXX_D83_R1_1																		67.4%	56%	151 bp	36%	25.0	6.2%	66.5%	56%	144 bp	18%	24.5
HVG3CDRXX_D83_R1_2																		65.1%	57%	151 bp	27%	25.0	4.4%
HVG3CDRXX_D8_R1	82.0	82.0	0.00%	0.05%	67.3%	1.20	19.6	13.6%	0.29%	42.8	39.2	100.0%	100.0%	7.2%	39.2	56.3%	11.4							77.3%	57%	146 bp	18%	20.1
HVG3CDRXX_D8_R1_1																		79.5%	58%	151 bp	36%	21.2	8.1%	78.3%	57%	146 bp	27%	20.1
HVG3CDRXX_D8_R1_2																		76.4%	59%	151 bp	27%	21.2	3.4%

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

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools	M Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	Biotype Counts	% rRNA	% reads overlapping rRNA features	`percent_rRNA`	None
\|\|	DupRadar	dupInt	Intercept value from DupRadar	`dupRadar_intercept`	None
\|\|	Picard	% Dups	Mark Duplicates - Percent Duplication	`PERCENT_DUPLICATION`	None
\|\|	QualiMap	5'-3' bias	5'-3' bias	`5_3_bias`	None
\|\|	QualiMap	M Aligned	Reads Aligned (millions)	`reads_aligned`	read_count
\|\|	RSeQC	% Proper Pairs	% Reads mapped in proper pairs	`proper_pairs_percent`	None
\|\|	Samtools	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`error_rate`	None
\|\|	Samtools	M Non-Primary	Non-primary alignments (millions)	`non-primary_alignments`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`reads_mapped`	read_count
\|\|	Samtools	% Mapped	% Mapped Reads	`reads_mapped_percent`	None
\|\|	Samtools	% Proper Pairs	% Properly Paired Reads	`reads_properly_paired_percent`	None
\|\|	Samtools	% MapQ 0 Reads	% of Reads that are Ambiguously Placed (MapQ=0)	`reads_MQ0_percent`	None
\|\|	Samtools	M Total seqs	Total sequences in the bam file (millions)	`raw_total_sequences`	read_count
\|\|	STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|	STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	read_count
\|\|	FastQC (raw)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (raw)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (raw)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (raw)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (raw)	M Seqs	Total Sequences (millions)	`total_sequences`	read_count
\|\|	Cutadapt	% BP Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None
\|\|	FastQC (trimmed)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (trimmed)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (trimmed)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (trimmed)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (trimmed)	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

Biotype Counts

shows reads overlapping genomic features of different biotypes, counted by featureCounts.

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DupRadar

provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication. This plot shows the general linear models - a summary of the gene duplication distributions.

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Picard

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

Mark Duplicates

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

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

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

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

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Preseq

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

Complexity curve

Note that the x axis is trimmed at the point where all the datasets show 80% of their maximum y-value, to avoid ridiculous scales.

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QualiMap

QualiMap is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Genomic origin of reads

Classification of mapped reads as originating in exonic, intronic or intergenic regions. These can be displayed as either the number or percentage of mapped reads.

There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. This allows mapped reads to be grouped by whether they originate in an exonic region (for QualiMap, this may include 5′ and 3′ UTR regions as well as protein-coding exons), an intron, or an intergenic region (see the Qualimap 2 documentation).

The inferred genomic origins of RNA-seq reads are presented here as a bar graph showing either the number or percentage of mapped reads in each read dataset that have been assigned to each type of genomic region. This graph can be used to assess the proportion of useful reads in an RNA-seq experiment. That proportion can be reduced by the presence of intron sequences, especially if depletion of ribosomal RNA was used during sample preparation (Sims et al. 2014). It can also be reduced by off-target transcripts, which are detected in greater numbers at the sequencing depths needed to detect poorly-expressed transcripts (Tarazona et al. 2011).

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Gene Coverage Profile

Mean distribution of coverage depth across the length of all mapped transcripts.

There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. QualiMap uses this information to calculate the depth of coverage along the length of each annotated transcript. For a set of reads mapped to a transcript, the depth of coverage at a given base position is the number of high-quality reads that map to the transcript at that position (Sims et al. 2014).

QualiMap calculates coverage depth at every base position of each annotated transcript. To enable meaningful comparison between transcripts, base positions are rescaled to relative positions expressed as percentage distance along each transcript (0%, 1%, …, 99%). For the set of transcripts with at least one mapped read, QualiMap plots the cumulative mapped-read depth (y-axis) at each relative transcript position (x-axis). This plot shows the gene coverage profile across all mapped transcripts for each read dataset. It provides a visual way to assess positional biases, such as an accumulation of mapped reads at the 3′ end of transcripts, which may indicate poor RNA quality in the original sample (Conesa et al. 2016).

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RSeQC

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

Read Distribution

Read Distribution calculates how mapped reads are distributed over genome features.

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Inner Distance

Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.

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Read Duplication

read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.

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Junction Annotation

Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.

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Junction Saturation

Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.

Click a line to see the data side by side (as in the original RSeQC plot).

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Infer experiment

Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

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Bam Stat

All numbers reported in millions.

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Samtools

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

Percent Mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

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Alignment metrics

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

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Samtools Flagstat

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

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XY counts

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Mapped reads per contig

The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

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STAR

STAR is an ultrafast universal RNA-seq aligner.

Alignment Scores

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FastQC (raw)

FastQC (raw) This section of the report shows FastQC results before adapter trimming.

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.

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.

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.

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Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

Filtered Reads

This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

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

Trimmed Sequence Lengths

This plot shows the number of reads with certain lengths of adapter trimmed.

Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

See the cutadapt documentation for more information on how these numbers are generated.

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

FastQC (trimmed)

FastQC (trimmed) This section of the report shows FastQC results after adapter trimming.

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

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:

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.

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.

No samples found with any adapter contamination > 0.1%

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.

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nf-core/rnaseq Software Versions

are collected at run time from the software output.

bedtools: 2.29.2
bioconductor-summarizedexperiment: 1.20.0
bioconductor-tximeta: 1.8.0
deseq2: 1.28.0
dupradar: 1.18.0
fastqc: 0.11.9
nextflow: 20.11.0-edge
nf-core/rnaseq: 3.0
picard: 2.23.9
preseq: 2.0.3
qualimap: 2.2.2-dev
rseqc: 3.0.1
salmon: 1.4.0
samtools: 1.10
star: 2.6.1d
stringtie: 2.1.4
subread: 2.0.1
trimgalore: 0.6.6
ucsc: 377

nf-core/rnaseq Workflow Summary

- this information is collected when the pipeline is started.

Core Nextflow options

revision: 3.0
runName: admiring_ramanujan
containerEngine: singularity
launchDir: /scratch/cgsb/gresham/mk5636
workDir: /scratch/cgsb/gresham/mk5636/HVG3CDRXX_merged/nextflow_work
projectDir: .nextflow/assets/nf-core/rnaseq
userName: mk5636
profile: singularity
configFiles: /scratch/cgsb/gresham/mk5636/.nextflow/assets/nf-core/rnaseq/nextflow.config, /scratch/cgsb/gresham/mk5636/HVG3CDRXX.config

Input/output options

input: /scratch/cgsb/gresham/mk5636/samplesheets/HVG3CDRXX_merged.csv
outdir: /scratch/cgsb/gresham/mk5636/HVG3CDRXX_merged/results
email: mk5636@nyu.edu

Reference genome options

fasta: /scratch/work/cgsb/genomes/Public/Vertebrate_mammalian/Homo_sapiens/Ensembl/GRCh38.p10/Homo_sapiens.GRCh38.dna.toplevel.fa
gtf: /scratch/work/cgsb/genomes/Public/Vertebrate_mammalian/Homo_sapiens/Ensembl/GRCh38.p10/Homo_sapiens.GRCh38.88.gtf
star_index: /scratch/cgsb/gresham/mk5636/HKVNYDRXX_1/results/genome/index/star

Generic options

tracedir: ./results/pipeline_info

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About MultiQC

General Statistics

General Statistics: Columns

Biotype Counts

DupRadar

Picard

Mark Duplicates Help

Preseq

Complexity curve

QualiMap

Genomic origin of reads Help

Gene Coverage Profile Help

RSeQC

Read Distribution

Inner Distance

Read Duplication

Junction Annotation

Junction Saturation

Infer experiment

Bam Stat

Samtools

Percent Mapped Help

Alignment metrics

Samtools Flagstat

XY counts

Mapped reads per contig

STAR

Alignment Scores

FastQC (raw)

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

Cutadapt

Filtered Reads

Trimmed Sequence Lengths Help

FastQC (trimmed)

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

nf-core/rnaseq Software Versions

nf-core/rnaseq Workflow Summary

v1.9

Highlight Samples

Rename Samples

Show / Hide Samples

Mark Duplicates

Genomic origin of reads

Gene Coverage Profile

Percent Mapped

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

Trimmed Sequence Lengths

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