MultiQC Report

General Statistics

Showing ²⁶⁵/₂₆₅ rows and ¹⁹/₂₂ columns.

Sample Name	M Reads	M Reads Mapped	dupInt	5'-3' bias	M Aligned	% Proper Pairs	% Dups	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs	% Aligned	M Aligned	% BP Trimmed	% Dups	% GC	Read Length	% Failed	M Seqs
SRX1125158	25.5	25.5	0.00%	1.13	9.5	47.0%	16.7%	0.11%	6.4	19.0	100.0%	100.0%	0.9%	19.0	74.4%	7.2
SRX1125158_1																	1.1%	47.1%	46%	100 bp	9%	9.6
SRX1125158_1_val_1																		46.8%	46%	99 bp	9%	9.6
SRX1125158_2																	1.6%	46.5%	46%	100 bp	9%	9.6
SRX1125158_2_val_2																		46.2%	46%	98 bp	9%	9.6
SRX1125159	19.7	19.7	0.00%	1.10	7.4	48.1%	16.0%	0.11%	4.8	14.9	100.0%	100.0%	0.7%	14.9	74.7%	5.6
SRX1125159_1																	1.1%	45.8%	46%	100 bp	9%	7.5
SRX1125159_1_val_1																		45.5%	46%	99 bp	9%	7.5
SRX1125159_2																	1.6%	45.2%	46%	100 bp	9%	7.5
SRX1125159_2_val_2																		44.9%	46%	98 bp	9%	7.5
SRX1125160	64.2	64.2	0.00%	1.19	22.3	43.5%	15.0%	0.12%	19.7	44.6	100.0%	100.0%	1.8%	44.6	72.0%	16.3
SRX1125160_1																	1.6%	50.9%	45%	100 bp	18%	22.7
SRX1125160_1_val_1																		50.4%	45%	98 bp	18%	22.6
SRX1125160_2																	2.2%	50.3%	45%	100 bp	18%	22.7
SRX1125160_2_val_2																		49.9%	45%	98 bp	9%	22.6
SRX1125162	72.0	72.0	0.00%	1.24	25.7	44.6%	15.0%	0.12%	20.6	51.3	100.0%	100.0%	1.3%	51.3	72.3%	18.8
SRX1125162_1																	1.6%	48.7%	45%	100 bp	9%	26.1
SRX1125162_1_val_1																		48.2%	45%	98 bp	9%	26.0
SRX1125162_2																	2.1%	48.1%	45%	100 bp	9%	26.1
SRX1125162_2_val_2																		47.6%	45%	98 bp	9%	26.0
SRX1125163	127.5	127.5	0.00%	1.15	44.7	38.4%	25.6%	0.11%	38.2	89.4	100.0%	100.0%	1.5%	89.4	71.7%	32.5
SRX1125163_1																	1.4%	61.9%	46%	100 bp	18%	45.5
SRX1125163_1_val_1																		61.5%	46%	98 bp	18%	45.3
SRX1125163_2																	1.9%	61.2%	46%	100 bp	18%	45.5
SRX1125163_2_val_2																		60.8%	46%	98 bp	18%	45.3
SRX1125164	86.1	86.1	0.00%	1.15	29.4	40.1%	20.2%	0.12%	27.2	58.8	100.0%	100.0%	2.0%	58.8	71.6%	21.4
SRX1125164_1																	1.9%	56.3%	46%	100 bp	18%	30.1
SRX1125164_1_val_1																		55.6%	46%	98 bp	18%	29.9
SRX1125164_2																	2.3%	55.3%	46%	100 bp	18%	30.1
SRX1125164_2_val_2																		54.9%	46%	98 bp	18%	29.9
SRX1125165	124.3	124.3	0.00%	1.08	41.7	35.3%	27.6%	0.11%	40.9	83.4	100.0%	100.0%	2.2%	83.4	70.6%	29.8
SRX1125165_1																	1.6%	62.6%	46%	100 bp	18%	42.5
SRX1125165_1_val_1																		62.1%	46%	98 bp	18%	42.3
SRX1125165_2																	2.1%	61.8%	46%	100 bp	18%	42.5
SRX1125165_2_val_2																		61.4%	46%	98 bp	18%	42.3
SRX1125166	26.0	26.0	0.01%	1.15	9.3	44.9%	15.5%	0.12%	7.3	18.7	100.0%	100.0%	1.3%	18.7	72.6%	6.9
SRX1125166_1																	1.7%	45.1%	46%	100 bp	9%	9.5
SRX1125166_1_val_1																		44.7%	46%	98 bp	9%	9.5
SRX1125166_2																	2.4%	44.5%	46%	100 bp	9%	9.5
SRX1125166_2_val_2																		44.1%	46%	98 bp	9%	9.5
SRX1125167	39.9	39.9	0.01%	1.40	6.5	16.4%	25.0%	0.15%	26.9	13.0	100.0%	100.0%	17.6%	13.0	47.1%	3.6
SRX1125167_1																	1.8%	51.3%	48%	100 bp	18%	7.7
SRX1125167_1_val_1																		50.7%	48%	98 bp	18%	7.6
SRX1125167_2																	2.9%	50.5%	48%	100 bp	18%	7.7
SRX1125167_2_val_2																		50.0%	48%	97 bp	9%	7.6
SRX1125168	31.6	31.6	0.01%	1.47	7.2	28.3%	12.9%	0.14%	17.1	14.5	100.0%	100.0%	8.7%	14.5	59.7%	4.7
SRX1125168_1																	1.6%	38.6%	47%	100 bp	9%	8.0
SRX1125168_1_val_1																		38.2%	47%	98 bp	9%	7.9
SRX1125168_2																	2.8%	37.8%	47%	100 bp	9%	8.0
SRX1125168_2_val_2																		37.3%	47%	97 bp	9%	7.9
SRX1125172	66.5	66.5	0.00%	1.44	12.4	21.1%	19.8%	0.14%	41.6	24.8	100.0%	100.0%	13.7%	24.8	53.8%	7.5
SRX1125172_1																	1.6%	49.2%	47%	100 bp	9%	14.1
SRX1125172_1_val_1																		48.7%	48%	98 bp	9%	14.0
SRX1125172_2																	2.6%	48.2%	47%	100 bp	9%	14.1
SRX1125172_2_val_2																		47.8%	47%	98 bp	9%	14.0
SRX1125173	48.1	48.1	0.00%	1.39	15.7	44.5%	6.8%	0.12%	16.6	31.5	100.0%	100.0%	2.5%	31.5	70.1%	11.3
SRX1125173_1																	1.6%	34.7%	45%	100 bp	9%	16.2
SRX1125173_1_val_1																		34.3%	45%	98 bp	9%	16.2
SRX1125173_2																	2.3%	33.9%	45%	100 bp	9%	16.2
SRX1125173_2_val_2																		33.6%	45%	98 bp	9%	16.2
SRX1125174	67.9	67.9	0.00%	1.37	16.8	30.6%	13.6%	0.13%	34.4	33.5	100.0%	100.0%	7.4%	33.5	61.8%	11.1
SRX1125174_1																	1.6%	43.6%	46%	100 bp	9%	18.1
SRX1125174_1_val_1																		43.1%	46%	98 bp	9%	18.0
SRX1125174_2																	2.4%	42.9%	46%	100 bp	9%	18.1
SRX1125174_2_val_2																		42.4%	46%	98 bp	9%	18.0
SRX1125175	53.9	53.9	0.00%	1.40	13.0	29.7%	13.1%	0.14%	27.9	26.0	100.0%	100.0%	7.7%	26.0	61.3%	8.6
SRX1125175_1																	1.7%	41.3%	46%	100 bp	9%	14.0
SRX1125175_1_val_1																		40.8%	46%	98 bp	9%	14.0
SRX1125175_2																	2.8%	40.3%	46%	100 bp	9%	14.0
SRX1125175_2_val_2																		39.7%	46%	97 bp	9%	14.0
SRX1125177	123.5	123.5	0.00%	1.43	12.5	5.8%	54.1%	0.19%	98.5	25.0	100.0%	100.0%	37.0%	25.0	25.3%	4.4
SRX1125177_1																	2.0%	76.4%	51%	100 bp	27%	17.6
SRX1125177_1_val_1																		75.8%	51%	98 bp	27%	17.4
SRX1125177_2																	3.4%	75.6%	51%	100 bp	27%	17.6
SRX1125177_2_val_2																		75.2%	51%	97 bp	27%	17.4
SRX1125179	106.0	106.0	0.00%	1.40	40.4	51.8%	9.6%	0.12%	25.1	80.9	100.0%	100.0%	0.5%	80.9	73.7%	30.3
SRX1125179_1																	1.3%	48.9%	44%	100 bp	9%	41.3
SRX1125179_1_val_1																		48.4%	44%	99 bp	9%	41.1
SRX1125179_2																	1.8%	48.1%	44%	100 bp	9%	41.3
SRX1125179_2_val_2																		47.8%	44%	98 bp	9%	41.1
SRX1125205	144.2	144.2	0.00%	1.37	54.1	48.6%	12.6%	0.11%	36.0	108.2	100.0%	100.0%	0.6%	108.2	72.8%	40.0
SRX1125205_1																	1.5%	53.1%	44%	100 bp	18%	55.2
SRX1125205_1_val_1																		52.7%	44%	98 bp	18%	54.9
SRX1125205_2																	1.9%	52.3%	44%	100 bp	18%	55.2
SRX1125205_2_val_2																		52.1%	44%	98 bp	18%	54.9
SRX1125208	75.9	75.9	0.01%	1.35	28.2	47.1%	14.9%	0.12%	19.5	56.4	100.0%	100.0%	0.9%	56.4	73.4%	21.1
SRX1125208_1																	1.4%	50.1%	44%	100 bp	18%	28.8
SRX1125208_1_val_1																		49.7%	44%	98 bp	9%	28.7
SRX1125208_2																	1.9%	49.4%	44%	100 bp	9%	28.8
SRX1125208_2_val_2																		49.1%	44%	98 bp	9%	28.7
SRX1125213	97.8	97.8	0.00%	1.28	37.0	46.9%	17.1%	0.12%	23.9	73.9	100.0%	100.0%	0.7%	73.9	74.4%	27.9
SRX1125213_1																	1.3%	52.9%	44%	100 bp	18%	37.6
SRX1125213_1_val_1																		52.6%	44%	98 bp	18%	37.5
SRX1125213_2																	1.8%	52.5%	44%	100 bp	18%	37.6
SRX1125213_2_val_2																		52.2%	44%	98 bp	18%	37.5
SRX1125215	81.6	81.6	0.01%	1.35	30.3	45.9%	16.9%	0.12%	21.1	60.5	100.0%	100.0%	1.0%	60.5	73.7%	22.7
SRX1125215_1																	1.3%	51.1%	44%	100 bp	18%	30.9
SRX1125215_1_val_1																		50.8%	44%	98 bp	18%	30.8
SRX1125215_2																	1.8%	50.6%	44%	100 bp	18%	30.9
SRX1125215_2_val_2																		50.3%	44%	98 bp	18%	30.8
SRX1125220	63.6	63.6	0.00%	1.18	15.5	28.7%	17.6%	0.13%	32.6	31.0	100.0%	100.0%	7.6%	31.0	61.0%	10.2
SRX1125220_1																	1.7%	53.7%	46%	100 bp	18%	16.9
SRX1125220_1_val_1																		53.2%	46%	98 bp	18%	16.8
SRX1125220_2																	2.5%	52.8%	46%	100 bp	18%	16.9
SRX1125220_2_val_2																		52.4%	46%	98 bp	18%	16.8
SRX1129649	59.8	59.8	0.00%	1.18	14.8	28.6%	18.4%	0.13%	30.2	29.6	100.0%	100.0%	7.2%	29.6	60.7%	9.7
SRX1129649_1																	2.0%	53.4%	46%	100 bp	18%	16.1
SRX1129649_1_val_1																		52.8%	46%	98 bp	18%	16.0
SRX1129649_2																	2.7%	52.8%	46%	100 bp	18%	16.1
SRX1129649_2_val_2																		52.3%	46%	97 bp	18%	16.0
SRX1129650	58.8	58.8	0.01%	1.21	9.4	14.9%	30.1%	0.16%	40.0	18.8	100.0%	100.0%	18.1%	18.8	45.7%	5.1
SRX1129650_1																	2.0%	60.9%	48%	100 bp	18%	11.2
SRX1129650_1_val_1																		60.3%	48%	98 bp	18%	11.1
SRX1129650_2																	3.1%	60.0%	48%	100 bp	18%	11.2
SRX1129650_2_val_2																		59.4%	48%	97 bp	18%	11.1
SRX1129660	150.1	150.1	0.01%	1.00	42.3	32.1%	21.2%	0.44%	65.4	84.6	100.0%	100.0%	5.4%	84.6	60.7%	28.9
SRX1129660_1																	0.7%	57.1%	47%	100 bp	9%	48.1
SRX1129660_1_val_1																		56.9%	47%	99 bp	18%	47.7
SRX1129660_2																	1.6%	53.2%	47%	81 bp	27%	48.1
SRX1129660_2_val_2																		53.1%	47%	80 bp	27%	47.7
SRX1129661	119.5	119.5	0.00%	1.04	38.6	40.0%	13.8%	0.38%	42.3	77.2	100.0%	100.0%	2.9%	77.2	60.7%	27.1
SRX1129661_1																	0.9%	52.9%	45%	100 bp	9%	45.0
SRX1129661_1_val_1																		52.2%	45%	99 bp	18%	44.6
SRX1129661_2																	2.2%	50.8%	45%	80 bp	9%	45.0
SRX1129661_2_val_2																		48.7%	45%	79 bp	9%	44.6
SRX1129662	141.2	141.2	0.00%	1.06	25.6	16.5%	30.1%	0.46%	89.9	51.2	100.0%	100.0%	15.9%	51.2	42.4%	13.8
SRX1129662_1																	0.7%	72.9%	50%	100 bp	9%	33.0
SRX1129662_1_val_1																		72.8%	50%	99 bp	18%	32.6
SRX1129662_2																	2.4%	70.8%	50%	80 bp	9%	33.0
SRX1129662_2_val_2																		70.8%	50%	79 bp	18%	32.6
SRX1129663	129.7	129.7	0.02%	1.24	21.9	15.6%	28.4%	0.67%	85.8	43.9	100.0%	100.0%	18.1%	43.9	41.9%	11.6
SRX1129663_1																	0.6%	64.7%	50%	100 bp	9%	28.1
SRX1129663_1_val_1																		64.7%	50%	99 bp	18%	27.8
SRX1129663_2																	1.8%	62.8%	50%	80 bp	18%	28.1
SRX1129663_2_val_2																		63.0%	50%	79 bp	27%	27.8
SRX1129664	36.9	36.9	0.00%	1.23	4.4	7.6%	33.0%	0.79%	28.0	8.8	100.0%	100.0%	31.0%	8.8	24.8%	1.6
SRX1129664_1																	0.6%	68.7%	54%	100 bp	9%	6.6
SRX1129664_1_val_1																		68.7%	54%	99 bp	18%	6.5
SRX1129664_2																	2.0%	67.3%	54%	80 bp	18%	6.6
SRX1129664_2_val_2																		67.3%	54%	79 bp	27%	6.5
SRX1129665	105.7	105.7	0.00%	1.18	35.3	41.1%	14.1%	0.41%	35.1	70.6	100.0%	99.9%	2.3%	70.6	60.3%	24.9
SRX1129665_1																	1.0%	56.4%	46%	100 bp	9%	41.7
SRX1129665_1_val_1																		55.6%	46%	99 bp	18%	41.2
SRX1129665_2																	2.6%	53.5%	46%	80 bp	9%	41.7
SRX1129665_2_val_2																		51.5%	46%	78 bp	18%	41.2
SRX1129666	81.3	81.3	0.00%	1.41	25.3	39.5%	14.7%	0.31%	30.6	50.7	100.0%	100.0%	3.6%	50.7	68.7%	18.4
SRX1129666_1																	0.4%	51.6%	46%	91 bp	20%	26.8
SRX1129666_1_val_1																		51.7%	46%	89 bp	20%	26.7
SRX1129666_2																	0.8%	48.2%	46%	91 bp	10%	26.8
SRX1129666_2_val_2																		48.4%	46%	89 bp	10%	26.7
SRX1129667	52.8	52.8	0.00%	1.22	17.0	42.1%	10.8%	0.31%	18.8	34.1	100.0%	100.0%	3.1%	34.1	66.8%	12.2
SRX1129667_1																	0.7%	50.5%	46%	100 bp	9%	18.4
SRX1129667_1_val_1																		50.4%	46%	99 bp	18%	18.3
SRX1129667_2																	2.0%	48.4%	46%	80 bp	0%	18.4
SRX1129667_2_val_2																		48.3%	46%	79 bp	9%	18.3
SRX1129670	42.8	42.8	0.00%	1.39	13.8	43.7%	7.0%	0.33%	15.2	27.6	100.0%	100.0%	3.0%	27.6	66.5%	9.8
SRX1129670_1																	0.7%	44.8%	46%	100 bp	0%	14.9
SRX1129670_1_val_1																		44.7%	46%	99 bp	9%	14.8
SRX1129670_2																	1.9%	43.0%	46%	80 bp	0%	14.9
SRX1129670_2_val_2																		42.9%	46%	79 bp	9%	14.8
SRX1129671	33.5	33.5	0.00%	1.36	9.8	38.6%	7.2%	0.35%	13.9	19.6	100.0%	100.0%	4.7%	19.6	62.7%	6.7
SRX1129671_1																	0.7%	41.3%	47%	100 bp	0%	10.9
SRX1129671_1_val_1																		41.1%	47%	99 bp	9%	10.7
SRX1129671_2																	2.2%	38.4%	47%	80 bp	0%	10.9
SRX1129671_2_val_2																		38.4%	47%	79 bp	9%	10.7
SRX1129672	41.9	41.9	0.00%	1.28	13.8	44.0%	8.2%	0.32%	14.2	27.7	100.0%	100.0%	2.6%	27.7	66.5%	9.8
SRX1129672_1																	0.7%	45.2%	46%	100 bp	0%	14.9
SRX1129672_1_val_1																		45.1%	46%	99 bp	9%	14.8
SRX1129672_2																	2.0%	42.4%	46%	80 bp	0%	14.9
SRX1129672_2_val_2																		42.5%	46%	79 bp	9%	14.8
SRX1129673	41.4	41.4	0.00%	1.32	14.0	46.5%	5.8%	0.31%	13.4	28.1	100.0%	100.0%	2.2%	28.1	66.8%	10.1
SRX1129673_1																	0.7%	40.6%	45%	100 bp	0%	15.2
SRX1129673_1_val_1																		40.5%	45%	99 bp	9%	15.1
SRX1129673_2																	2.1%	38.8%	45%	80 bp	0%	15.2
SRX1129673_2_val_2																		38.7%	45%	79 bp	9%	15.1
SRX1129714	217.2	217.2	0.02%	1.25	41.2	18.3%	28.6%	0.47%	134.7	82.5	100.0%	100.0%	14.8%	82.5	46.1%	23.5
SRX1129714_1																	0.6%	68.6%	49%	100 bp	9%	51.5
SRX1129714_1_val_1																		68.5%	50%	99 bp	18%	51.0
SRX1129714_2																	1.9%	66.9%	50%	80 bp	18%	51.5
SRX1129714_2_val_2																		67.0%	50%	79 bp	27%	51.0
SRX1129715	48.9	48.9	0.00%	1.34	16.8	47.7%	5.5%	0.32%	15.4	33.5	100.0%	100.0%	2.1%	33.5	67.9%	12.1
SRX1129715_1																	0.7%	43.6%	45%	100 bp	0%	18.1
SRX1129715_1_val_1																		43.5%	45%	99 bp	9%	17.9
SRX1129715_2																	2.2%	41.6%	45%	80 bp	0%	18.1
SRX1129715_2_val_2																		41.6%	45%	79 bp	9%	17.9
SRX1130446	64.5	64.5	0.00%	1.25	23.4	47.0%	12.8%	0.27%	17.7	46.8	100.0%	100.0%	1.2%	46.8	70.0%	17.3
SRX1130446_1																	0.7%	49.3%	45%	100 bp	0%	24.9
SRX1130446_1_val_1																		49.3%	45%	99 bp	9%	24.7
SRX1130446_2																	1.8%	47.6%	45%	80 bp	0%	24.9
SRX1130446_2_val_2																		47.5%	45%	79 bp	9%	24.7
SRX1130447	51.8	51.8	0.00%	1.27	17.6	45.8%	7.3%	0.31%	16.7	35.1	100.0%	100.0%	2.1%	35.1	67.0%	12.6
SRX1130447_1																	0.8%	48.1%	45%	100 bp	0%	19.0
SRX1130447_1_val_1																		47.9%	45%	99 bp	9%	18.8
SRX1130447_2																	2.0%	45.9%	45%	80 bp	0%	19.0
SRX1130447_2_val_2																		45.8%	45%	79 bp	9%	18.8
SRX1130448	78.8	78.8	0.00%	1.25	26.9	44.5%	11.1%	0.32%	25.1	53.7	100.0%	100.0%	2.1%	53.7	67.6%	19.3
SRX1130448_1																	0.7%	50.7%	45%	100 bp	9%	28.8
SRX1130448_1_val_1																		50.7%	45%	99 bp	18%	28.5
SRX1130448_2																	2.0%	48.1%	45%	80 bp	0%	28.8
SRX1130448_2_val_2																		48.1%	45%	79 bp	9%	28.5
SRX1130449	76.5	76.5	0.00%	1.35	27.1	45.5%	14.9%	0.32%	22.3	54.2	100.0%	100.0%	1.6%	54.2	71.8%	20.2
SRX1130449_1																	0.4%	49.5%	44%	91 bp	10%	28.3
SRX1130449_1_val_1																		49.4%	45%	89 bp	10%	28.2
SRX1130449_2																	0.7%	46.1%	44%	91 bp	10%	28.3
SRX1130449_2_val_2																		46.0%	45%	89 bp	10%	28.2
SRX1130508	64.7	64.7	0.01%	1.40	23.4	45.6%	11.8%	0.26%	17.8	46.9	100.0%	100.0%	0.9%	46.9	61.5%	16.7
SRX1130508_1																	0.8%	50.1%	45%	100 bp	9%	27.3
SRX1130508_1_val_1																		49.8%	45%	99 bp	9%	27.1
SRX1130508_2																	1.7%	49.3%	45%	80 bp	0%	27.3
SRX1130508_2_val_2																		48.6%	45%	79 bp	9%	27.1
SRX1130519	28.6	28.6	0.00%	1.34	9.8	47.7%	6.0%	0.33%	9.0	19.6	100.0%	99.9%	2.1%	19.6	68.6%	7.1
SRX1130519_1																	0.7%	42.7%	45%	100 bp	0%	10.5
SRX1130519_1_val_1																		42.6%	45%	99 bp	9%	10.4
SRX1130519_2																	2.0%	39.6%	45%	80 bp	0%	10.5
SRX1130519_2_val_2																		39.5%	45%	79 bp	9%	10.4
SRX1130520	53.6	53.6	0.00%	1.30	19.0	46.7%	10.3%	0.33%	15.6	38.0	100.0%	100.0%	1.5%	38.0	67.9%	13.7
SRX1130520_1																	0.7%	48.6%	45%	100 bp	0%	20.4
SRX1130520_1_val_1																		48.5%	45%	99 bp	9%	20.2
SRX1130520_2																	2.0%	46.5%	45%	80 bp	0%	20.4
SRX1130520_2_val_2																		46.4%	45%	79 bp	9%	20.2
SRX1130521	100.9	100.9	0.00%	1.24	36.3	46.5%	13.3%	0.31%	28.2	72.7	100.0%	100.0%	1.3%	72.7	69.8%	26.7
SRX1130521_1																	0.7%	56.7%	44%	100 bp	9%	38.6
SRX1130521_1_val_1																		56.7%	45%	99 bp	18%	38.3
SRX1130521_2																	2.0%	54.9%	45%	80 bp	9%	38.6
SRX1130521_2_val_2																		54.8%	45%	79 bp	18%	38.3
SRX1130522	109.2	109.2	0.02%	1.55	38.3	40.5%	22.6%	0.19%	32.6	76.6	100.0%	100.0%	1.3%	76.6	70.7%	27.5
SRX1130522_1																	1.0%	54.7%	46%	100 bp	27%	39.0
SRX1130522_1_val_1																		54.5%	46%	99 bp	27%	38.8
SRX1130522_2																	1.4%	56.0%	46%	100 bp	18%	39.0
SRX1130522_2_val_2																		56.0%	46%	99 bp	18%	38.8
SRX1130523	115.8	115.8	0.02%	1.55	34.3	36.0%	18.1%	0.20%	47.2	68.5	100.0%	100.0%	4.1%	68.5	68.4%	24.4
SRX1130523_1																	1.2%	51.2%	46%	100 bp	27%	36.0
SRX1130523_1_val_1																		50.9%	46%	99 bp	27%	35.7
SRX1130523_2																	1.6%	52.4%	46%	100 bp	18%	36.0
SRX1130523_2_val_2																		52.4%	46%	99 bp	18%	35.7
SRX1130524	103.4	103.4	0.02%	1.44	31.9	32.9%	28.0%	0.20%	39.5	63.9	100.0%	100.0%	3.1%	63.9	67.1%	22.1
SRX1130524_1																	1.4%	56.8%	46%	100 bp	27%	33.2
SRX1130524_1_val_1																		56.5%	47%	99 bp	27%	32.9
SRX1130524_2																	1.7%	58.1%	46%	100 bp	18%	33.2
SRX1130524_2_val_2																		58.2%	46%	99 bp	18%	32.9
SRX1130527	137.7	137.7	0.00%	1.49	42.5	26.5%	41.2%	0.20%	52.6	85.1	100.0%	100.0%	2.9%	85.1	64.5%	28.1
SRX1130527_1																	1.1%	64.6%	47%	100 bp	27%	43.8
SRX1130527_1_val_1																		64.4%	47%	99 bp	27%	43.6
SRX1130527_2																	1.5%	66.5%	47%	100 bp	18%	43.8
SRX1130527_2_val_2																		66.5%	47%	99 bp	18%	43.6
SRX1130528	94.0	94.0	0.04%	1.56	22.9	18.2%	47.4%	0.22%	48.2	45.9	100.0%	100.0%	7.3%	45.9	59.3%	14.5
SRX1130528_1																	1.6%	67.2%	48%	100 bp	18%	24.8
SRX1130528_1_val_1																		66.9%	48%	99 bp	27%	24.5
SRX1130528_2																	1.9%	68.7%	48%	100 bp	18%	24.8
SRX1130528_2_val_2																		68.9%	48%	99 bp	18%	24.5
SRX1130529	158.4	158.4	0.02%	1.53	42.7	25.1%	36.0%	0.20%	73.1	85.3	100.0%	100.0%	5.7%	85.3	63.8%	28.8
SRX1130529_1																	1.3%	63.4%	47%	100 bp	27%	45.4
SRX1130529_1_val_1																		63.2%	47%	99 bp	27%	45.1
SRX1130529_2																	1.6%	64.8%	47%	100 bp	18%	45.4
SRX1130529_2_val_2																		64.8%	47%	99 bp	18%	45.1
SRX1130530	39.6	39.6	0.08%	1.57	7.8	17.1%	37.8%	0.23%	23.9	15.6	100.0%	100.0%	11.8%	15.6	55.7%	4.9
SRX1130530_1																	1.5%	60.6%	49%	100 bp	18%	8.9
SRX1130530_1_val_1																		60.3%	49%	99 bp	27%	8.8
SRX1130530_2																	1.9%	62.1%	49%	100 bp	9%	8.9
SRX1130530_2_val_2																		62.3%	49%	99 bp	18%	8.8
SRX1130531	147.6	147.6	0.06%	1.45	25.8	14.7%	40.2%	0.23%	95.9	51.7	100.0%	100.0%	15.6%	51.7	51.0%	15.1
SRX1130531_1																	1.0%	65.5%	49%	100 bp	27%	29.8
SRX1130531_1_val_1																		65.4%	49%	99 bp	27%	29.6
SRX1130531_2																	1.5%	67.3%	49%	100 bp	18%	29.8
SRX1130531_2_val_2																		67.3%	49%	99 bp	18%	29.6

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
\|\|	DupRadar	dupInt	Intercept value from DupRadar	`dupRadar_intercept`	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
\|\|	Picard	% Dups	Mark Duplicates - Percent Duplication	`PERCENT_DUPLICATION`	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
\|\|	Cutadapt	% BP Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Read Length	Average Read Length (bp)	`avg_sequence_length`	None
\|\|	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

nf-core/rnaseq Software Versions

are collected at run time from the software output.

Process Name	Software	Version
`BEDTOOLS_GENOMECOV`	`bedtools`	`2.30.0`
`CUSTOM_DUMPSOFTWAREVERSIONS`	`python`	`3.10.6`
	`yaml`	`6.0`
`CUSTOM_GETCHROMSIZES`	`getchromsizes`	`1.16.1`
`DESEQ2_QC_STAR_SALMON`	`bioconductor-deseq2`	`1.28.0`
	`r-base`	`4.0.3`
`DUPRADAR`	`bioconductor-dupradar`	`1.28.0`
	`r-base`	`4.2.1`
`FASTQC`	`fastqc`	`0.11.9`
`FQ_SUBSAMPLE`	`fq`	`0.9.1 (2022-02-22)`
`GTF2BED`	`perl`	`5.26.2`
`GTF_GENE_FILTER`	`python`	`3.9.5`
`GUNZIP_FASTA`	`gunzip`	`1.10`
`MAKE_TRANSCRIPTS_FASTA`	`rsem`	`1.3.1`
	`star`	`2.7.10a`
`PICARD_MARKDUPLICATES`	`picard`	`2.27.4-SNAPSHOT`
`QUALIMAP_RNASEQ`	`qualimap`	`2.2.2-dev`
`RSEQC_BAMSTAT`	`rseqc`	`3.0.1`
`RSEQC_INFEREXPERIMENT`	`rseqc`	`3.0.1`
`RSEQC_INNERDISTANCE`	`rseqc`	`3.0.1`
`RSEQC_JUNCTIONANNOTATION`	`rseqc`	`3.0.1`
`RSEQC_JUNCTIONSATURATION`	`rseqc`	`3.0.1`
`RSEQC_READDISTRIBUTION`	`rseqc`	`3.0.1`
`RSEQC_READDUPLICATION`	`rseqc`	`3.0.1`
`SALMON_INDEX`	`salmon`	`1.9.0`
`SALMON_QUANT`	`salmon`	`1.9.0`
`SALMON_SE_GENE`	`bioconductor-summarizedexperiment`	`1.24.0`
	`r-base`	`4.1.1`
`SALMON_TX2GENE`	`python`	`3.9.5`
`SALMON_TXIMPORT`	`bioconductor-tximeta`	`1.12.0`
	`r-base`	`4.1.1`
`SAMPLESHEET_CHECK`	`python`	`3.9.5`
`SAMTOOLS_FLAGSTAT`	`samtools`	`1.16.1`
`SAMTOOLS_IDXSTATS`	`samtools`	`1.16.1`
`SAMTOOLS_INDEX`	`samtools`	`1.16.1`
`SAMTOOLS_SORT`	`samtools`	`1.16.1`
`SAMTOOLS_STATS`	`samtools`	`1.16.1`
`STAR_ALIGN`	`gawk`	`5.1.0`
	`samtools`	`1.16.1`
	`star`	`2.7.9a`
`STAR_GENOMEGENERATE`	`gawk`	`5.1.0`
	`samtools`	`1.16.1`
	`star`	`2.7.9a`
`STRINGTIE_STRINGTIE`	`stringtie`	`2.2.1`
`TRIMGALORE`	`cutadapt`	`3.4`
	`trimgalore`	`0.6.7`
`UCSC_BEDCLIP`	`ucsc`	`377`
`UCSC_BEDGRAPHTOBIGWIG`	`ucsc`	`377`
`Workflow`	`Nextflow`	`22.10.7`
	`nf-core/rnaseq`	`3.10.1`

nf-core/rnaseq Workflow Summary

- this information is collected when the pipeline is started.

Core Nextflow options

revision: master
runName: disturbed_yonath
containerEngine: singularity
launchDir: /data/adf/nf-core/rnaseq
workDir: /data/adf/nf-core/rnaseq/work
projectDir: /home/adf/.nextflow/assets/nf-core/rnaseq
userName: adf
profile: singularity
configFiles: /home/adf/.nextflow/assets/nf-core/rnaseq/nextflow.config

Input/output options

input: arahy_clevenger_2016/samplesheet/samplesheet.csv
outdir: arahy_clevenger_2016

Reference genome options

fasta: /erdos/legumeinfo/data/v2/Arachis/hypogaea/genomes/Tifrunner.gnm2.J5K5/arahy.Tifrunner.gnm2.J5K5.genome_main.fna.gz
gtf: arahy.Tifrunner.gnm2.ann2.PVFB.gene_models_main.gtf

Generic options

multiqc_config: arahy_clevenger_2016/samplesheet/multiqc_config.yaml

nf-core/rnaseq Methods Description

Suggested text and references to use when describing pipeline usage within the methods section of a publication.

Methods

Data was processed using nf-core/rnaseq v3.10.1 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020).

The pipeline was executed with Nextflow v22.10.7 (Di Tommaso et al., 2017) with the following command:

nextflow run nf-core/rnaseq -profile singularity --input arahy_clevenger_2016/samplesheet/samplesheet.csv --fasta /erdos/legumeinfo/data/v2/Arachis/hypogaea/genomes/Tifrunner.gnm2.J5K5/arahy.Tifrunner.gnm2.J5K5.genome_main.fna.gz --gtf arahy.Tifrunner.gnm2.ann2.PVFB.gene_models_main.gtf --outdir arahy_clevenger_2016 --multiqc_config arahy_clevenger_2016/samplesheet/multiqc_config.yaml

References

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x

Notes:

The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

STAR_SALMON DESeq2 PCA plot

PCA plot between samples in the experiment. These values are calculated using DESeq2 in the deseq2_qc.r script.

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STAR_SALMON DESeq2 sample similarity

is generated from clustering by Euclidean distances between DESeq2 rlog values for each sample in the deseq2_qc.r script.

Min:

Max:

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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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QualiMap

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

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).

The Normalised plot is calculated by MultiQC to enable comparison of samples with varying sequencing depth. The cumulative mapped-read depth at each position across the averaged transcript position are divided by the total for that sample across the entire averaged transcript.

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RSeQC

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.DOI: 10.1093/bioinformatics/bts356.

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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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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Samtools

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

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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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.DOI: 10.1093/bioinformatics/bts635.

Alignment Scores

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Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.DOI: 10.14806/ej.17.1.200.

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 (3')

This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

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

FastQC 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

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.

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Status Checks

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

FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

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

In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

Min:

Max:

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STAR_SALMON DESeq2 PCA plot

STAR_SALMON DESeq2 sample similarity

DupRadar

QualiMap

Genomic origin of reads Help

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RSeQC

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Mapped reads per contig

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Per Sequence Quality Scores Help

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Per Sequence GC Content Help

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Sequence Duplication Levels Help

Overrepresented sequences Help

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v1.13

Highlight Samples

Rename Samples

Show / Hide Samples

Genomic origin of reads

Gene Coverage Profile

Mark Duplicates

Percent Mapped

Trimmed Sequence Lengths (3')

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