20260603_LH00166_0309_A23WCJNLT4

MultiQC Report for DAQ. Includes data from all the QC tools in DAQ.

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Report generated on 2026-06-08, 18:20 UTC based on data in: /tmp/nxf.sSOaHRcqZR

Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

General Statistics

Showing ²⁸⁸/₂₈₈ rows and ¹⁷/₃₁ columns.

Sample Name	≥ 1X	≥ 5X	≥ 10X	≥ 30X	≥ 50X	Median	Mean Cov.	Min Cov.	Max Cov.	Mb Total Coverage Bases	Genome length	Fold Enrichment	Target Bases ≥ 30X	Duplication	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Mean insert	% Duplication	% > Q30	Mb Q30 bases	Reads After Filtering	GC content	% PF	% Adapter	Mean R1 Length	Mean R2 Length
Filler-D0000335	100.0%	100.0%	100.0%	100.0%	99.0%	425X	471.5X	0.0X	87691.0X	18494.8Mb	39227450	42X	98%	83.6%	0.37%	0.0M	2274.3M	100.0%	96.8%	4.5%	2274.3M	232.7bp
Filler-D0000335_S20_L001																							32.6%	97.4%	40868.7Mb	283.0M	51.7%	99.1%	9.8%	150.0bp	150.0bp
Filler-D0000335_S20_L002																							30.7%	97.5%	40988.4Mb	283.4M	51.7%	99.2%	9.7%	150.0bp	150.0bp
Filler-D0000335_S20_L003																							29.6%	97.4%	41038.0Mb	284.3M	51.8%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0000335_S20_L004																							33.4%	97.5%	40804.9Mb	282.3M	51.8%	99.2%	9.8%	150.0bp	150.0bp
Filler-D0000335_S20_L005																							33.1%	97.5%	40874.8Mb	282.9M	51.8%	99.2%	9.9%	150.0bp	150.0bp
Filler-D0000335_S20_L006																							32.5%	97.5%	41376.5Mb	286.4M	51.8%	99.2%	10.0%	150.0bp	150.0bp
Filler-D0000335_S20_L007																							32.9%	97.5%	41438.0Mb	286.8M	51.8%	99.2%	10.0%	150.0bp	150.0bp
Filler-D0000335_S20_L008																							32.7%	97.5%	41222.6Mb	285.3M	51.8%	99.2%	10.0%	150.0bp	150.0bp
Filler-D0000539	100.0%	100.0%	100.0%	100.0%	99.0%	408X	447.6X	0.0X	76726.0X	17558.8Mb	39227450	41X	99%	86.5%	0.37%	0.0M	2650.1M	100.0%	97.2%	4.2%	2650.2M	242.0bp
Filler-D0000539_S23_L001																							37.1%	97.3%	47532.7Mb	329.2M	51.1%	99.1%	9.1%	150.0bp	150.0bp
Filler-D0000539_S23_L002																							35.2%	97.4%	47807.9Mb	330.7M	51.1%	99.1%	8.9%	150.0bp	150.0bp
Filler-D0000539_S23_L003																							34.0%	97.3%	48204.0Mb	334.0M	51.2%	99.1%	9.2%	150.0bp	150.0bp
Filler-D0000539_S23_L004																							38.3%	97.4%	48455.0Mb	335.3M	51.2%	99.1%	9.0%	150.0bp	150.0bp
Filler-D0000539_S23_L005																							37.7%	97.4%	47488.7Mb	328.7M	51.2%	99.1%	9.2%	150.0bp	150.0bp
Filler-D0000539_S23_L006																							36.9%	97.4%	47748.5Mb	330.6M	51.2%	99.1%	9.4%	150.0bp	150.0bp
Filler-D0000539_S23_L007																							37.2%	97.4%	47856.8Mb	331.3M	51.2%	99.1%	9.4%	150.0bp	150.0bp
Filler-D0000539_S23_L008																							37.1%	97.4%	47709.3Mb	330.3M	51.2%	99.1%	9.3%	150.0bp	150.0bp
Filler-D0000637	100.0%	100.0%	100.0%	99.0%	99.0%	364X	400.2X	0.0X	84653.0X	15697.3Mb	39227450	40X	98%	84.6%	0.39%	0.0M	2054.4M	100.0%	97.2%	4.4%	2054.4M	263.4bp
Filler-D0000637_S13_L001																							36.4%	97.3%	37083.5Mb	256.9M	51.6%	99.0%	8.1%	150.0bp	150.0bp
Filler-D0000637_S13_L002																							35.0%	97.4%	37287.3Mb	258.0M	51.6%	99.1%	7.9%	150.0bp	150.0bp
Filler-D0000637_S13_L003																							33.2%	97.3%	36933.4Mb	256.0M	51.6%	99.0%	8.3%	150.0bp	150.0bp
Filler-D0000637_S13_L004																							37.2%	97.4%	36992.1Mb	256.1M	51.6%	99.1%	8.0%	150.0bp	150.0bp
Filler-D0000637_S13_L005																							36.8%	97.4%	36878.7Mb	255.4M	51.6%	99.1%	8.2%	150.0bp	150.0bp
Filler-D0000637_S13_L006																							35.9%	97.4%	37163.7Mb	257.4M	51.6%	99.1%	8.4%	150.0bp	150.0bp
Filler-D0000637_S13_L007																							36.1%	97.4%	37169.5Mb	257.4M	51.6%	99.1%	8.4%	150.0bp	150.0bp
Filler-D0000637_S13_L008																							36.1%	97.4%	37133.7Mb	257.1M	51.6%	99.1%	8.3%	150.0bp	150.0bp
Filler-D0000789	100.0%	100.0%	100.0%	100.0%	99.0%	468X	525.9X	0.0X	90578.0X	20629.5Mb	39227450	40X	99%	81.3%	0.36%	0.0M	2154.8M	100.0%	97.4%	4.4%	2154.8M	257.1bp
Filler-D0000789_S10_L001																							32.6%	97.3%	38773.1Mb	268.4M	51.7%	99.1%	7.8%	150.0bp	150.0bp
Filler-D0000789_S10_L002																							31.5%	97.4%	39159.3Mb	270.8M	51.7%	99.1%	7.6%	150.0bp	150.0bp
Filler-D0000789_S10_L003																							29.7%	97.2%	38555.1Mb	267.0M	51.7%	99.1%	7.9%	150.0bp	150.0bp
Filler-D0000789_S10_L004																							33.3%	97.3%	38458.1Mb	266.1M	51.7%	99.1%	7.7%	150.0bp	150.0bp
Filler-D0000789_S10_L005																							32.9%	97.3%	38820.9Mb	268.6M	51.7%	99.1%	7.8%	150.0bp	150.0bp
Filler-D0000789_S10_L006																							32.1%	97.3%	39362.8Mb	272.4M	51.7%	99.1%	8.0%	150.0bp	150.0bp
Filler-D0000789_S10_L007																							32.4%	97.3%	39311.6Mb	272.0M	51.7%	99.1%	8.0%	150.0bp	150.0bp
Filler-D0000789_S10_L008																							32.2%	97.3%	38944.8Mb	269.5M	51.7%	99.2%	8.0%	150.0bp	150.0bp
Filler-D0000861	100.0%	100.0%	100.0%	99.0%	99.0%	261X	301.0X	0.0X	75828.0X	11806.0Mb	39227450	41X	98%	78.0%	0.37%	0.0M	1030.9M	100.0%	97.7%	4.2%	1031.0M	253.2bp
Filler-D0000861_S14_L001																							29.5%	97.3%	18520.5Mb	128.2M	51.3%	99.1%	8.2%	150.0bp	150.0bp
Filler-D0000861_S14_L002																							28.7%	97.4%	18624.7Mb	128.7M	51.3%	99.1%	8.0%	150.0bp	150.0bp
Filler-D0000861_S14_L003																							26.8%	97.3%	18416.6Mb	127.5M	51.4%	99.1%	8.4%	150.0bp	150.0bp
Filler-D0000861_S14_L004																							30.2%	97.4%	18288.4Mb	126.5M	51.4%	99.1%	8.2%	150.0bp	150.0bp
Filler-D0000861_S14_L005																							29.9%	97.4%	18584.1Mb	128.5M	51.4%	99.2%	8.3%	150.0bp	150.0bp
Filler-D0000861_S14_L006																							29.2%	97.4%	18974.7Mb	131.3M	51.4%	99.2%	8.5%	150.0bp	150.0bp
Filler-D0000861_S14_L007																							29.3%	97.4%	18911.1Mb	130.8M	51.4%	99.2%	8.5%	150.0bp	150.0bp
Filler-D0000861_S14_L008																							29.2%	97.4%	18724.5Mb	129.5M	51.4%	99.2%	8.4%	150.0bp	150.0bp
Filler-D0000890	100.0%	100.0%	100.0%	99.0%	99.0%	240X	252.9X	0.0X	67372.0X	9920.7Mb	39227450	40X	98%	86.4%	0.39%	0.0M	1586.3M	100.0%	96.9%	4.2%	1586.3M	262.1bp
Filler-D0000890_S21_L001																							38.2%	97.2%	28627.2Mb	198.6M	51.3%	98.9%	8.6%	150.0bp	150.0bp
Filler-D0000890_S21_L002																							36.4%	97.3%	28666.0Mb	198.7M	51.4%	99.0%	8.4%	150.0bp	150.0bp
Filler-D0000890_S21_L003																							34.9%	97.2%	28732.4Mb	199.5M	51.4%	99.0%	8.8%	150.0bp	150.0bp
Filler-D0000890_S21_L004																							39.2%	97.3%	28995.3Mb	201.1M	51.4%	99.0%	8.5%	150.0bp	150.0bp
Filler-D0000890_S21_L005																							38.5%	97.3%	28417.6Mb	197.1M	51.4%	99.0%	8.7%	150.0bp	150.0bp
Filler-D0000890_S21_L006																							37.5%	97.3%	28412.3Mb	197.1M	51.4%	99.0%	8.9%	150.0bp	150.0bp
Filler-D0000890_S21_L007																							37.8%	97.3%	28414.1Mb	197.1M	51.4%	99.0%	8.9%	150.0bp	150.0bp
Filler-D0000890_S21_L008																							37.9%	97.3%	28429.0Mb	197.2M	51.4%	99.0%	8.8%	150.0bp	150.0bp
Filler-D0001009	100.0%	100.0%	100.0%	100.0%	99.0%	315X	340.8X	0.0X	69868.0X	13366.7Mb	39227450	36X	99%	84.9%	0.38%	0.0M	1819.4M	100.0%	96.8%	4.1%	1819.4M	325.6bp
Filler-D0001009_S8_L001																							40.1%	96.9%	33024.0Mb	229.1M	51.0%	98.9%	5.6%	150.0bp	150.0bp
Filler-D0001009_S8_L002																							39.4%	96.9%	33630.4Mb	233.2M	51.0%	98.9%	5.4%	150.0bp	150.0bp
Filler-D0001009_S8_L003																							36.9%	96.8%	32424.7Mb	225.2M	51.1%	98.9%	5.8%	150.0bp	150.0bp
Filler-D0001009_S8_L004																							40.8%	96.9%	32887.5Mb	228.2M	51.1%	98.9%	5.6%	150.0bp	150.0bp
Filler-D0001009_S8_L005																							40.2%	96.9%	32688.2Mb	226.8M	51.1%	98.9%	5.7%	150.0bp	150.0bp
Filler-D0001009_S8_L006																							39.0%	96.9%	32566.4Mb	225.9M	51.1%	98.9%	5.9%	150.0bp	150.0bp
Filler-D0001009_S8_L007																							39.2%	96.9%	32525.0Mb	225.6M	51.1%	98.9%	5.9%	150.0bp	150.0bp
Filler-D0001009_S8_L008																							39.2%	97.0%	32517.4Mb	225.5M	51.1%	98.9%	5.9%	150.0bp	150.0bp
Filler-D0001089	100.0%	100.0%	100.0%	100.0%	99.0%	430X	468.8X	0.0X	77996.0X	18388.7Mb	39227450	43X	98%	81.9%	0.38%	0.0M	2089.7M	100.0%	88.9%	4.7%	2089.8M	217.8bp
Filler-D0001089_S16_L001																							30.9%	97.5%	37829.8Mb	261.4M	51.2%	99.1%	8.8%	150.0bp	150.0bp
Filler-D0001089_S16_L002																							29.0%	97.7%	37759.0Mb	260.6M	51.2%	99.2%	8.7%	150.0bp	150.0bp
Filler-D0001089_S16_L003																							27.8%	97.5%	37545.6Mb	259.6M	51.3%	99.2%	8.9%	150.0bp	150.0bp
Filler-D0001089_S16_L004																							31.4%	97.6%	37325.9Mb	257.8M	51.3%	99.2%	8.8%	150.0bp	150.0bp
Filler-D0001089_S16_L005																							31.2%	97.6%	37617.7Mb	259.8M	51.3%	99.2%	8.8%	150.0bp	150.0bp
Filler-D0001089_S16_L006																							30.7%	97.6%	38210.1Mb	264.0M	51.3%	99.2%	9.0%	150.0bp	150.0bp
Filler-D0001089_S16_L007																							31.0%	97.6%	38228.5Mb	264.0M	51.3%	99.2%	9.0%	150.0bp	150.0bp
Filler-D0001089_S16_L008																							30.8%	97.6%	38030.9Mb	262.7M	51.3%	99.2%	8.9%	150.0bp	150.0bp
Filler-D0001104	100.0%	100.0%	100.0%	99.0%	99.0%	300X	318.1X	0.0X	78763.0X	12478.5Mb	39227450	40X	98%	83.7%	0.39%	0.0M	1602.4M	100.0%	97.5%	3.9%	1602.4M	266.3bp
Filler-D0001104_S9_L001																							35.6%	97.2%	29082.7Mb	201.4M	50.8%	99.0%	7.7%	150.0bp	150.0bp
Filler-D0001104_S9_L002																							34.3%	97.3%	29234.8Mb	202.3M	50.9%	99.0%	7.5%	150.0bp	150.0bp
Filler-D0001104_S9_L003																							32.5%	97.2%	28708.3Mb	198.9M	50.9%	99.0%	7.9%	150.0bp	150.0bp
Filler-D0001104_S9_L004																							36.3%	97.3%	28694.7Mb	198.6M	50.9%	99.0%	7.7%	150.0bp	150.0bp
Filler-D0001104_S9_L005																							35.9%	97.3%	28794.0Mb	199.3M	50.9%	99.1%	7.8%	150.0bp	150.0bp
Filler-D0001104_S9_L006																							35.0%	97.3%	29003.2Mb	200.8M	50.9%	99.0%	8.0%	150.0bp	150.0bp
Filler-D0001104_S9_L007																							35.2%	97.3%	28959.7Mb	200.5M	50.9%	99.1%	8.0%	150.0bp	150.0bp
Filler-D0001104_S9_L008																							35.2%	97.3%	28993.2Mb	200.7M	50.9%	99.1%	8.0%	150.0bp	150.0bp
Filler-D0001215	100.0%	100.0%	100.0%	99.0%	99.0%	326X	355.7X	0.0X	85621.0X	13954.6Mb	39227450	40X	98%	87.2%	0.38%	0.0M	2255.2M	100.0%	97.1%	4.2%	2255.3M	254.5bp
Filler-D0001215_S7_L001																							38.5%	97.3%	40481.8Mb	280.7M	50.8%	99.0%	9.1%	150.0bp	150.0bp
Filler-D0001215_S7_L002																							36.5%	97.4%	40705.5Mb	281.9M	50.8%	99.1%	8.9%	150.0bp	150.0bp
Filler-D0001215_S7_L003																							35.2%	97.3%	40918.0Mb	283.9M	50.9%	99.1%	9.3%	150.0bp	150.0bp
Filler-D0001215_S7_L004																							39.5%	97.4%	41031.4Mb	284.3M	50.9%	99.1%	9.1%	150.0bp	150.0bp
Filler-D0001215_S7_L005																							39.0%	97.4%	40406.0Mb	280.1M	50.9%	99.1%	9.2%	150.0bp	150.0bp
Filler-D0001215_S7_L006																							38.1%	97.4%	40570.7Mb	281.3M	50.9%	99.1%	9.4%	150.0bp	150.0bp
Filler-D0001215_S7_L007																							38.5%	97.4%	40651.7Mb	281.8M	50.9%	99.1%	9.4%	150.0bp	150.0bp
Filler-D0001215_S7_L008																							38.4%	97.4%	40600.1Mb	281.4M	50.9%	99.1%	9.4%	150.0bp	150.0bp
Filler-D0001322	100.0%	100.0%	100.0%	100.0%	99.0%	371X	407.6X	0.0X	73412.0X	15990.2Mb	39227450	39X	99%	84.1%	0.35%	0.0M	2028.6M	100.0%	97.2%	4.2%	2028.6M	283.1bp
Filler-D0001322_S19_L001																							37.6%	97.2%	36816.9Mb	254.8M	51.1%	99.0%	6.6%	150.0bp	150.0bp
Filler-D0001322_S19_L002																							36.6%	97.2%	37314.9Mb	258.0M	51.1%	99.0%	6.4%	150.0bp	150.0bp
Filler-D0001322_S19_L003																							34.4%	97.1%	36302.7Mb	251.4M	51.1%	99.0%	6.7%	150.0bp	150.0bp
Filler-D0001322_S19_L004																							38.3%	97.2%	36471.8Mb	252.3M	51.1%	99.0%	6.5%	150.0bp	150.0bp
Filler-D0001322_S19_L005																							37.8%	97.2%	36532.4Mb	252.8M	51.1%	99.1%	6.7%	150.0bp	150.0bp
Filler-D0001322_S19_L006																							36.7%	97.2%	36615.3Mb	253.3M	51.1%	99.0%	6.8%	150.0bp	150.0bp
Filler-D0001322_S19_L007																							37.0%	97.2%	36598.8Mb	253.2M	51.1%	99.0%	6.8%	150.0bp	150.0bp
Filler-D0001322_S19_L008																							37.0%	97.2%	36537.7Mb	252.7M	51.1%	99.1%	6.8%	150.0bp	150.0bp
Filler-D0001361	100.0%	100.0%	100.0%	100.0%	99.0%	258X	294.6X	0.0X	69547.0X	11556.8Mb	39227450	40X	98%	77.2%	0.39%	0.0M	986.1M	100.0%	97.2%	4.4%	986.1M	269.0bp
Filler-D0001361_S2_L001																							30.8%	97.2%	17782.6Mb	123.3M	51.5%	99.1%	9.0%	150.0bp	150.0bp
Filler-D0001361_S2_L002																							30.4%	97.3%	18060.5Mb	125.1M	51.5%	99.1%	8.8%	150.0bp	150.0bp
Filler-D0001361_S2_L003																							28.1%	97.2%	17462.5Mb	121.2M	51.5%	99.1%	9.2%	150.0bp	150.0bp
Filler-D0001361_S2_L004																							31.4%	97.3%	17406.5Mb	120.6M	51.5%	99.1%	8.9%	150.0bp	150.0bp
Filler-D0001361_S2_L005																							31.0%	97.3%	17826.7Mb	123.5M	51.5%	99.1%	9.1%	150.0bp	150.0bp
Filler-D0001361_S2_L006																							30.0%	97.3%	18025.7Mb	124.9M	51.5%	99.1%	9.4%	150.0bp	150.0bp
Filler-D0001361_S2_L007																							30.2%	97.3%	17944.4Mb	124.4M	51.5%	99.1%	9.4%	150.0bp	150.0bp
Filler-D0001361_S2_L008																							30.1%	97.3%	17761.7Mb	123.1M	51.5%	99.1%	9.3%	150.0bp	150.0bp
Filler-D0001515	100.0%	100.0%	100.0%	100.0%	99.0%	331X	358.5X	0.0X	81594.0X	14064.6Mb	39227450	39X	99%	87.0%	0.38%	0.0M	2260.6M	100.0%	96.8%	4.2%	2260.7M	286.6bp
Filler-D0001515_S17_L001																							39.2%	96.9%	40497.1Mb	281.6M	50.7%	99.0%	7.8%	150.0bp	150.0bp
Filler-D0001515_S17_L002																							37.5%	97.0%	40896.4Mb	284.2M	50.7%	99.0%	7.6%	150.0bp	150.0bp
Filler-D0001515_S17_L003																							35.8%	96.9%	40366.0Mb	281.0M	50.8%	99.0%	8.0%	150.0bp	150.0bp
Filler-D0001515_S17_L004																							39.8%	97.0%	40222.3Mb	279.7M	50.8%	99.0%	7.8%	150.0bp	150.0bp
Filler-D0001515_S17_L005																							39.7%	97.0%	40553.0Mb	281.9M	50.8%	99.0%	7.9%	150.0bp	150.0bp
Filler-D0001515_S17_L006																							38.9%	97.0%	41002.5Mb	285.0M	50.8%	99.0%	8.1%	150.0bp	150.0bp
Filler-D0001515_S17_L007																							39.2%	97.0%	40953.8Mb	284.7M	50.8%	99.0%	8.1%	150.0bp	150.0bp
Filler-D0001515_S17_L008																							39.1%	97.0%	40662.5Mb	282.6M	50.8%	99.0%	8.1%	150.0bp	150.0bp
Filler-D0002474	100.0%	100.0%	100.0%	99.0%	99.0%	339X	364.4X	0.0X	58330.0X	14293.5Mb	39227450	39X	98%	86.5%	0.34%	0.0M	2185.8M	100.0%	97.4%	4.0%	2185.9M	276.1bp
Filler-D0002474_S18_L001																							39.5%	97.2%	39448.0Mb	273.1M	50.7%	98.9%	7.0%	150.0bp	150.0bp
Filler-D0002474_S18_L002																							38.1%	97.3%	39801.0Mb	275.2M	50.7%	99.0%	6.8%	150.0bp	150.0bp
Filler-D0002474_S18_L003																							36.3%	97.2%	39619.8Mb	274.4M	50.8%	99.0%	7.1%	150.0bp	150.0bp
Filler-D0002474_S18_L004																							40.6%	97.3%	40099.6Mb	277.4M	50.8%	99.0%	6.9%	150.0bp	150.0bp
Filler-D0002474_S18_L005																							39.8%	97.3%	39206.4Mb	271.3M	50.8%	99.0%	7.0%	150.0bp	150.0bp
Filler-D0002474_S18_L006																							38.7%	97.3%	39158.4Mb	271.0M	50.8%	99.0%	7.2%	150.0bp	150.0bp
Filler-D0002474_S18_L007																							39.0%	97.3%	39202.9Mb	271.3M	50.8%	99.0%	7.2%	150.0bp	150.0bp
Filler-D0002474_S18_L008																							39.1%	97.3%	39322.5Mb	272.1M	50.8%	99.0%	7.2%	150.0bp	150.0bp
Filler-D0002530	100.0%	100.0%	100.0%	100.0%	99.0%	421X	465.7X	0.0X	64323.0X	18268.1Mb	39227450	42X	98%	83.9%	0.33%	0.0M	2302.1M	100.0%	96.4%	4.5%	2302.2M	232.6bp
Filler-D0002530_S12_L001																							33.5%	97.4%	41237.5Mb	286.0M	51.9%	99.1%	10.2%	150.0bp	150.0bp
Filler-D0002530_S12_L002																							31.7%	97.5%	41338.9Mb	286.3M	51.9%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0002530_S12_L003																							30.4%	97.4%	41311.1Mb	286.7M	52.0%	99.1%	10.3%	150.0bp	150.0bp
Filler-D0002530_S12_L004																							34.2%	97.5%	41050.3Mb	284.5M	52.0%	99.2%	10.1%	150.0bp	150.0bp
Filler-D0002530_S12_L005																							34.1%	97.5%	41328.4Mb	286.5M	52.0%	99.2%	10.3%	150.0bp	150.0bp
Filler-D0002530_S12_L006																							33.5%	97.5%	42036.9Mb	291.5M	52.0%	99.2%	10.4%	150.0bp	150.0bp
Filler-D0002530_S12_L007																							33.8%	97.5%	42055.4Mb	291.6M	52.0%	99.2%	10.4%	150.0bp	150.0bp
Filler-D0002530_S12_L008																							33.5%	97.5%	41697.1Mb	289.1M	52.0%	99.2%	10.4%	150.0bp	150.0bp
Filler-D0002564	100.0%	100.0%	100.0%	99.0%	99.0%	270X	287.8X	0.0X	84416.0X	11290.2Mb	39227450	37X	98%	86.1%	0.40%	0.0M	1741.1M	100.0%	96.8%	4.2%	1741.1M	305.9bp
Filler-D0002564_S24_L001																							40.0%	96.9%	31389.9Mb	218.2M	50.8%	98.9%	6.9%	150.0bp	150.0bp
Filler-D0002564_S24_L002																							39.0%	96.9%	31879.4Mb	221.4M	50.8%	98.9%	6.7%	150.0bp	150.0bp
Filler-D0002564_S24_L003																							36.7%	96.8%	30991.5Mb	215.6M	50.9%	98.9%	7.1%	150.0bp	150.0bp
Filler-D0002564_S24_L004																							40.8%	96.9%	31201.0Mb	216.9M	50.9%	98.9%	6.9%	150.0bp	150.0bp
Filler-D0002564_S24_L005																							40.4%	96.9%	31247.1Mb	217.2M	50.9%	98.9%	7.0%	150.0bp	150.0bp
Filler-D0002564_S24_L006																							39.3%	96.9%	31355.9Mb	217.9M	50.9%	98.9%	7.2%	150.0bp	150.0bp
Filler-D0002564_S24_L007																							39.5%	97.0%	31271.3Mb	217.3M	50.9%	98.9%	7.2%	150.0bp	150.0bp
Filler-D0002564_S24_L008																							39.5%	97.0%	31163.9Mb	216.5M	50.9%	98.9%	7.2%	150.0bp	150.0bp
Filler-D0002693	100.0%	100.0%	100.0%	100.0%	99.0%	309X	331.1X	0.0X	75828.0X	12988.2Mb	39227450	38X	99%	88.9%	0.37%	0.0M	2480.9M	100.0%	97.0%	3.9%	2481.0M	303.1bp
Filler-D0002693_S11_L001																							43.1%	97.0%	44754.6Mb	310.6M	50.5%	99.0%	6.9%	150.0bp	150.0bp
Filler-D0002693_S11_L002																							41.4%	97.0%	45278.4Mb	314.0M	50.5%	99.0%	6.7%	150.0bp	150.0bp
Filler-D0002693_S11_L003																							39.6%	96.9%	44897.4Mb	311.8M	50.6%	99.0%	7.0%	150.0bp	150.0bp
Filler-D0002693_S11_L004																							44.2%	97.0%	45683.1Mb	317.0M	50.6%	99.0%	6.8%	150.0bp	150.0bp
Filler-D0002693_S11_L005																							43.4%	97.0%	44428.6Mb	308.3M	50.6%	99.0%	7.0%	150.0bp	150.0bp
Filler-D0002693_S11_L006																							42.3%	97.0%	44101.8Mb	306.0M	50.6%	99.0%	7.2%	150.0bp	150.0bp
Filler-D0002693_S11_L007																							42.7%	97.0%	44203.2Mb	306.7M	50.6%	99.0%	7.2%	150.0bp	150.0bp
Filler-D0002693_S11_L008																							42.7%	97.0%	44196.4Mb	306.6M	50.6%	99.0%	7.2%	150.0bp	150.0bp
Filler-D0002805	100.0%	100.0%	100.0%	99.0%	99.0%	254X	268.6X	0.0X	72197.0X	10536.9Mb	39227450	38X	98%	87.2%	0.39%	0.0M	1795.2M	100.0%	97.0%	4.1%	1795.2M	301.8bp
Filler-D0002805_S15_L001																							39.9%	96.9%	32489.2Mb	225.4M	50.5%	99.0%	6.2%	150.0bp	150.0bp
Filler-D0002805_S15_L002																							38.3%	96.9%	32897.9Mb	228.1M	50.6%	99.0%	6.0%	150.0bp	150.0bp
Filler-D0002805_S15_L003																							36.5%	96.8%	32524.0Mb	225.8M	50.6%	99.0%	6.3%	150.0bp	150.0bp
Filler-D0002805_S15_L004																							41.0%	96.9%	33144.4Mb	229.9M	50.6%	99.0%	6.1%	150.0bp	150.0bp
Filler-D0002805_S15_L005																							40.2%	96.9%	32193.7Mb	223.4M	50.6%	99.0%	6.3%	150.0bp	150.0bp
Filler-D0002805_S15_L006																							39.0%	96.9%	31848.7Mb	220.9M	50.6%	99.0%	6.4%	150.0bp	150.0bp
Filler-D0002805_S15_L007																							39.4%	96.9%	31877.4Mb	221.1M	50.6%	99.0%	6.4%	150.0bp	150.0bp
Filler-D0002805_S15_L008																							39.3%	97.0%	31796.4Mb	220.5M	50.6%	99.0%	6.4%	150.0bp	150.0bp
Filler-D0002881	100.0%	100.0%	100.0%	100.0%	99.0%	360X	390.7X	0.0X	51947.0X	15326.1Mb	39227450	41X	98%	81.0%	0.35%	0.0M	1651.8M	100.0%	97.3%	4.4%	1651.9M	240.2bp
Filler-D0002881_S22_L001																							31.3%	97.4%	29738.2Mb	206.2M	51.2%	99.0%	9.7%	150.0bp	150.0bp
Filler-D0002881_S22_L002																							30.0%	97.5%	29706.2Mb	205.7M	51.2%	99.0%	9.5%	150.0bp	150.0bp
Filler-D0002881_S22_L003																							28.4%	97.3%	29735.5Mb	206.3M	51.2%	99.0%	9.9%	150.0bp	150.0bp
Filler-D0002881_S22_L004																							32.1%	97.4%	29636.9Mb	205.4M	51.3%	99.1%	9.6%	150.0bp	150.0bp
Filler-D0002881_S22_L005																							31.6%	97.4%	29580.3Mb	205.0M	51.2%	99.1%	9.8%	150.0bp	150.0bp
Filler-D0002881_S22_L006																							30.8%	97.4%	29958.1Mb	207.7M	51.2%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0002881_S22_L007																							31.1%	97.4%	29962.9Mb	207.7M	51.2%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0002881_S22_L008																							31.1%	97.4%	29991.3Mb	207.9M	51.2%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0002923	100.0%	100.0%	100.0%	99.0%	99.0%	346X	373.7X	0.0X	82798.0X	14659.3Mb	39227450	40X	98%	81.4%	0.38%	0.0M	1602.3M	100.0%	97.2%	4.2%	1602.4M	264.3bp
Filler-D0002923_S32_L001																							32.9%	97.2%	28974.0Mb	200.5M	51.3%	99.0%	7.5%	150.0bp	150.0bp
Filler-D0002923_S32_L002																							31.8%	97.3%	29099.3Mb	201.2M	51.3%	99.1%	7.3%	150.0bp	150.0bp
Filler-D0002923_S32_L003																							29.9%	97.2%	28740.4Mb	199.0M	51.4%	99.0%	7.7%	150.0bp	150.0bp
Filler-D0002923_S32_L004																							33.6%	97.3%	28794.9Mb	199.2M	51.4%	99.1%	7.5%	150.0bp	150.0bp
Filler-D0002923_S32_L005																							33.2%	97.3%	28786.6Mb	199.1M	51.4%	99.1%	7.6%	150.0bp	150.0bp
Filler-D0002923_S32_L006																							32.3%	97.3%	29103.8Mb	201.4M	51.4%	99.1%	7.8%	150.0bp	150.0bp
Filler-D0002923_S32_L007																							32.6%	97.3%	29066.2Mb	201.1M	51.4%	99.1%	7.8%	150.0bp	150.0bp
Filler-D0002923_S32_L008																							32.5%	97.3%	29040.4Mb	200.9M	51.4%	99.1%	7.7%	150.0bp	150.0bp
Filler-D0002999	100.0%	100.0%	100.0%	100.0%	99.0%	416X	465.1X	0.0X	88928.0X	18242.6Mb	39227450	43X	98%	87.0%	0.36%	0.0M	2880.8M	100.0%	93.5%	4.7%	2880.9M	221.5bp
Filler-D0002999_S31_L001																							36.6%	97.4%	51218.2Mb	357.3M	52.0%	99.1%	14.1%	150.0bp	150.0bp
Filler-D0002999_S31_L002																							34.2%	97.6%	51169.1Mb	356.5M	52.0%	99.1%	13.8%	150.0bp	150.0bp
Filler-D0002999_S31_L003																							33.4%	97.4%	52113.8Mb	363.7M	52.1%	99.1%	14.2%	150.0bp	150.0bp
Filler-D0002999_S31_L004																							37.8%	97.5%	52059.6Mb	362.9M	52.1%	99.1%	13.9%	150.0bp	150.0bp
Filler-D0002999_S31_L005																							37.3%	97.5%	51243.0Mb	357.3M	52.1%	99.2%	14.2%	150.0bp	150.0bp
Filler-D0002999_S31_L006																							36.6%	97.5%	51691.8Mb	360.6M	52.1%	99.1%	14.4%	150.0bp	150.0bp
Filler-D0002999_S31_L007																							37.0%	97.5%	51843.4Mb	361.6M	52.1%	99.2%	14.4%	150.0bp	150.0bp
Filler-D0002999_S31_L008																							36.9%	97.5%	51750.6Mb	361.0M	52.1%	99.2%	14.4%	150.0bp	150.0bp
Filler-D0003090	100.0%	100.0%	100.0%	100.0%	99.0%	396X	437.7X	0.0X	80161.0X	17169.5Mb	39227450	41X	99%	81.8%	0.37%	0.0M	1907.0M	100.0%	97.5%	4.4%	1907.0M	251.4bp
Filler-D0003090_S28_L001																							32.6%	97.2%	34240.8Mb	238.3M	52.5%	99.0%	10.5%	150.0bp	150.0bp
Filler-D0003090_S28_L002																							31.4%	97.3%	34472.3Mb	239.6M	52.5%	99.0%	10.3%	150.0bp	150.0bp
Filler-D0003090_S28_L003																							29.6%	97.2%	33867.4Mb	235.8M	52.6%	99.0%	10.7%	150.0bp	150.0bp
Filler-D0003090_S28_L004																							33.2%	97.3%	33724.1Mb	234.6M	52.6%	99.0%	10.5%	150.0bp	150.0bp
Filler-D0003090_S28_L005																							32.9%	97.3%	34175.1Mb	237.7M	52.6%	99.1%	10.6%	150.0bp	150.0bp
Filler-D0003090_S28_L006																							32.1%	97.3%	34673.6Mb	241.2M	52.6%	99.0%	10.9%	150.0bp	150.0bp
Filler-D0003090_S28_L007																							32.4%	97.3%	34610.6Mb	240.8M	52.6%	99.1%	10.9%	150.0bp	150.0bp
Filler-D0003090_S28_L008																							32.2%	97.3%	34374.1Mb	239.1M	52.6%	99.1%	10.8%	150.0bp	150.0bp
Filler-D0003105	100.0%	100.0%	100.0%	99.0%	99.0%	324X	346.6X	0.0X	53680.0X	13595.9Mb	39227450	40X	98%	84.7%	0.36%	0.0M	1858.5M	100.0%	97.3%	4.3%	1858.5M	253.3bp
Filler-D0003105_S30_L001																							35.4%	97.2%	33589.8Mb	233.0M	52.0%	99.0%	9.1%	150.0bp	150.0bp
Filler-D0003105_S30_L002																							33.8%	97.3%	33771.3Mb	234.0M	52.0%	99.0%	8.9%	150.0bp	150.0bp
Filler-D0003105_S30_L003																							32.1%	97.2%	33301.2Mb	231.1M	52.1%	99.0%	9.3%	150.0bp	150.0bp
Filler-D0003105_S30_L004																							36.1%	97.3%	33287.7Mb	230.7M	52.1%	99.0%	9.1%	150.0bp	150.0bp
Filler-D0003105_S30_L005																							35.8%	97.3%	33355.5Mb	231.2M	52.1%	99.0%	9.2%	150.0bp	150.0bp
Filler-D0003105_S30_L006																							34.9%	97.3%	33583.1Mb	232.9M	52.1%	99.0%	9.4%	150.0bp	150.0bp
Filler-D0003105_S30_L007																							35.2%	97.3%	33630.3Mb	233.2M	52.1%	99.0%	9.4%	150.0bp	150.0bp
Filler-D0003105_S30_L008																							35.2%	97.3%	33551.6Mb	232.6M	52.1%	99.0%	9.4%	150.0bp	150.0bp
Filler-D0003157	100.0%	100.0%	100.0%	100.0%	99.0%	442X	493.7X	0.0X	90803.0X	19367.6Mb	39227450	40X	99%	78.8%	0.38%	0.0M	1777.9M	100.0%	97.2%	4.4%	1777.9M	262.1bp
Filler-D0003157_S26_L001																							31.2%	97.2%	32109.2Mb	221.9M	51.8%	99.0%	6.4%	150.0bp	150.0bp
Filler-D0003157_S26_L002																							30.3%	97.3%	32337.9Mb	223.3M	51.8%	99.0%	6.2%	150.0bp	150.0bp
Filler-D0003157_S26_L003																							28.5%	97.2%	31736.4Mb	219.5M	51.9%	99.0%	6.5%	150.0bp	150.0bp
Filler-D0003157_S26_L004																							31.9%	97.3%	31641.5Mb	218.6M	51.9%	99.0%	6.3%	150.0bp	150.0bp
Filler-D0003157_S26_L005																							31.4%	97.3%	32158.0Mb	222.1M	51.9%	99.0%	6.4%	150.0bp	150.0bp
Filler-D0003157_S26_L006																							30.6%	97.3%	32698.8Mb	225.9M	51.8%	99.0%	6.6%	150.0bp	150.0bp
Filler-D0003157_S26_L007																							30.7%	97.3%	32522.8Mb	224.7M	51.9%	99.0%	6.6%	150.0bp	150.0bp
Filler-D0003157_S26_L008																							30.6%	97.3%	32134.2Mb	222.0M	51.9%	99.0%	6.6%	150.0bp	150.0bp
Filler-D0003224	100.0%	100.0%	100.0%	100.0%	99.0%	354X	383.0X	0.0X	57707.0X	15024.2Mb	39227450	40X	98%	83.6%	0.35%	0.0M	1877.3M	100.0%	97.1%	4.4%	1877.3M	260.5bp
Filler-D0003224_S27_L001																							34.2%	97.2%	33896.7Mb	235.6M	52.6%	99.0%	9.7%	150.0bp	150.0bp
Filler-D0003224_S27_L002																							32.8%	97.3%	34175.7Mb	237.3M	52.6%	99.0%	9.5%	150.0bp	150.0bp
Filler-D0003224_S27_L003																							31.1%	97.2%	33506.8Mb	233.1M	52.7%	99.0%	9.9%	150.0bp	150.0bp
Filler-D0003224_S27_L004																							34.9%	97.2%	33476.9Mb	232.6M	52.7%	99.0%	9.7%	150.0bp	150.0bp
Filler-D0003224_S27_L005																							34.6%	97.2%	33646.2Mb	233.8M	52.6%	99.1%	9.8%	150.0bp	150.0bp
Filler-D0003224_S27_L006																							33.7%	97.3%	33862.6Mb	235.3M	52.6%	99.0%	10.0%	150.0bp	150.0bp
Filler-D0003224_S27_L007																							34.0%	97.3%	33860.8Mb	235.3M	52.7%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0003224_S27_L008																							33.9%	97.3%	33721.0Mb	234.3M	52.7%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0003241	100.0%	100.0%	100.0%	100.0%	99.0%	369X	403.6X	0.0X	74140.0X	15833.1Mb	39227450	41X	98%	82.2%	0.38%	0.0M	1810.1M	100.0%	97.3%	4.3%	1810.1M	248.1bp
Filler-D0003241_S25_L001																							32.8%	97.3%	32638.8Mb	226.6M	52.5%	99.0%	10.2%	150.0bp	150.0bp
Filler-D0003241_S25_L002																							31.5%	97.4%	32776.3Mb	227.3M	52.4%	99.1%	10.0%	150.0bp	150.0bp
Filler-D0003241_S25_L003																							29.8%	97.3%	32326.9Mb	224.6M	52.5%	99.1%	10.3%	150.0bp	150.0bp
Filler-D0003241_S25_L004																							33.4%	97.4%	32259.4Mb	223.9M	52.5%	99.1%	10.1%	150.0bp	150.0bp
Filler-D0003241_S25_L005																							33.1%	97.4%	32448.5Mb	225.2M	52.5%	99.1%	10.3%	150.0bp	150.0bp
Filler-D0003241_S25_L006																							32.3%	97.4%	32799.9Mb	227.7M	52.5%	99.1%	10.5%	150.0bp	150.0bp
Filler-D0003241_S25_L007																							32.6%	97.4%	32785.4Mb	227.6M	52.5%	99.1%	10.5%	150.0bp	150.0bp
Filler-D0003241_S25_L008																							32.5%	97.4%	32720.1Mb	227.1M	52.5%	99.1%	10.4%	150.0bp	150.0bp
Filler-D0003441	100.0%	100.0%	100.0%	99.0%	99.0%	314X	334.5X	0.0X	74917.0X	13120.1Mb	39227450	40X	98%	88.6%	0.37%	0.0M	2437.5M	100.0%	96.9%	4.2%	2437.5M	255.2bp
Filler-D0003441_S29_L001																							40.5%	97.3%	43716.3Mb	303.4M	51.4%	99.0%	8.7%	150.0bp	150.0bp
Filler-D0003441_S29_L002																							38.3%	97.4%	43980.7Mb	304.8M	51.5%	99.0%	8.5%	150.0bp	150.0bp
Filler-D0003441_S29_L003																							37.0%	97.3%	44010.7Mb	305.6M	51.5%	99.0%	8.8%	150.0bp	150.0bp
Filler-D0003441_S29_L004																							41.4%	97.3%	43992.6Mb	305.1M	51.5%	99.0%	8.6%	150.0bp	150.0bp
Filler-D0003441_S29_L005																							41.1%	97.3%	43698.7Mb	303.1M	51.5%	99.1%	8.7%	150.0bp	150.0bp
Filler-D0003441_S29_L006																							40.3%	97.4%	44008.9Mb	305.3M	51.5%	99.0%	8.9%	150.0bp	150.0bp
Filler-D0003441_S29_L007																							40.7%	97.4%	44118.5Mb	306.0M	51.5%	99.0%	8.9%	150.0bp	150.0bp
Filler-D0003441_S29_L008																							40.6%	97.4%	43847.5Mb	304.1M	51.5%	99.1%	8.9%	150.0bp	150.0bp
T13-D0003360	100.0%	100.0%	100.0%	100.0%	99.0%	298X	319.5X	0.0X	59622.0X	12532.5Mb	39227450	40X	98%	89.8%	0.34%	0.0M	2627.4M	100.0%	97.6%	4.3%	2627.5M	260.1bp
T13-D0003360_S1_L001																							42.9%	97.3%	47094.9Mb	327.4M	52.5%	99.1%	10.5%	150.0bp	150.0bp
T13-D0003360_S1_L002																							40.6%	97.4%	47387.5Mb	329.0M	52.5%	99.1%	10.3%	150.0bp	150.0bp
T13-D0003360_S1_L003																							39.2%	97.2%	47397.8Mb	329.7M	52.6%	99.1%	10.7%	150.0bp	150.0bp
T13-D0003360_S1_L004																							43.9%	97.3%	47747.0Mb	331.7M	52.5%	99.1%	10.4%	150.0bp	150.0bp
T13-D0003360_S1_L005																							43.4%	97.3%	46928.6Mb	326.1M	52.5%	99.1%	10.6%	150.0bp	150.0bp
T13-D0003360_S1_L006																							42.6%	97.3%	47110.1Mb	327.5M	52.5%	99.1%	10.9%	150.0bp	150.0bp
T13-D0003360_S1_L007																							43.0%	97.4%	47238.0Mb	328.3M	52.6%	99.1%	10.9%	150.0bp	150.0bp
T13-D0003360_S1_L008																							42.9%	97.4%	47142.4Mb	327.6M	52.6%	99.2%	10.8%	150.0bp	150.0bp
T18-D0001467	100.0%	100.0%	100.0%	100.0%	99.0%	351X	399.1X	0.0X	112483.0X	15657.6Mb	39227450	34X	99%	83.2%	0.41%	0.0M	1909.3M	100.0%	95.4%	4.0%	1909.4M	366.3bp
T18-D0001467_S3_L001																							40.6%	96.3%	34472.4Mb	239.9M	49.9%	98.7%	3.8%	150.0bp	150.0bp
T18-D0001467_S3_L002																							40.6%	96.3%	35372.1Mb	246.1M	49.9%	98.8%	3.6%	150.0bp	150.0bp
T18-D0001467_S3_L003																							37.5%	96.2%	33713.2Mb	234.9M	50.0%	98.7%	3.9%	150.0bp	150.0bp
T18-D0001467_S3_L004																							41.3%	96.3%	34188.0Mb	238.0M	50.0%	98.8%	3.7%	150.0bp	150.0bp
T18-D0001467_S3_L005																							40.7%	96.3%	34334.4Mb	239.0M	49.9%	98.8%	3.8%	150.0bp	150.0bp
T18-D0001467_S3_L006																							39.4%	96.4%	34218.6Mb	238.0M	49.9%	98.8%	4.0%	150.0bp	150.0bp
T18-D0001467_S3_L007																							39.6%	96.4%	34075.1Mb	237.0M	50.0%	98.8%	4.0%	150.0bp	150.0bp
T18-D0001467_S3_L008																							39.6%	96.4%	33976.3Mb	236.3M	49.9%	98.8%	4.0%	150.0bp	150.0bp
T18-D0003255	100.0%	100.0%	100.0%	99.0%	99.0%	366X	401.0X	0.0X	71573.0X	15729.2Mb	39227450	39X	99%	88.3%	0.35%	0.0M	2767.9M	100.0%	97.0%	4.1%	2768.0M	277.7bp
T18-D0003255_S4_L001																							41.1%	97.1%	49657.4Mb	344.2M	52.0%	99.0%	7.3%	150.0bp	150.0bp
T18-D0003255_S4_L002																							39.2%	97.2%	50288.4Mb	348.2M	52.0%	99.1%	7.1%	150.0bp	150.0bp
T18-D0003255_S4_L003																							37.8%	97.1%	50314.2Mb	348.9M	52.0%	99.0%	7.4%	150.0bp	150.0bp
T18-D0003255_S4_L004																							42.3%	97.2%	50968.9Mb	353.1M	52.0%	99.1%	7.2%	150.0bp	150.0bp
T18-D0003255_S4_L005																							41.6%	97.2%	49638.7Mb	343.9M	52.0%	99.1%	7.4%	150.0bp	150.0bp
T18-D0003255_S4_L006																							40.6%	97.2%	49462.3Mb	342.7M	52.0%	99.1%	7.6%	150.0bp	150.0bp
T18-D0003255_S4_L007																							40.9%	97.2%	49594.2Mb	343.6M	52.0%	99.1%	7.6%	150.0bp	150.0bp
T18-D0003255_S4_L008																							40.9%	97.2%	49568.5Mb	343.4M	52.0%	99.1%	7.6%	150.0bp	150.0bp
T21-D0003322	100.0%	100.0%	100.0%	100.0%	99.0%	340X	367.2X	0.0X	77001.0X	14404.5Mb	39227450	40X	98%	85.4%	0.37%	0.0M	2026.3M	100.0%	97.0%	4.1%	2026.4M	264.0bp
T21-D0003322_S5_L001																							37.4%	97.3%	36480.0Mb	253.1M	52.2%	99.0%	9.0%	150.0bp	150.0bp
T21-D0003322_S5_L002																							35.9%	97.3%	36781.8Mb	255.0M	52.2%	99.1%	8.8%	150.0bp	150.0bp
T21-D0003322_S5_L003																							34.1%	97.2%	36293.2Mb	252.0M	52.3%	99.1%	9.2%	150.0bp	150.0bp
T21-D0003322_S5_L004																							38.1%	97.3%	36369.1Mb	252.3M	52.3%	99.1%	9.0%	150.0bp	150.0bp
T21-D0003322_S5_L005																							37.8%	97.3%	36378.4Mb	252.3M	52.3%	99.1%	9.1%	150.0bp	150.0bp
T21-D0003322_S5_L006																							36.9%	97.3%	36646.5Mb	254.2M	52.3%	99.1%	9.3%	150.0bp	150.0bp
T21-D0003322_S5_L007																							37.1%	97.3%	36639.8Mb	254.2M	52.3%	99.1%	9.3%	150.0bp	150.0bp
T21-D0003322_S5_L008																							37.1%	97.3%	36513.1Mb	253.3M	52.3%	99.1%	9.3%	150.0bp	150.0bp
T21-D0003376	100.0%	100.0%	100.0%	100.0%	99.0%	385X	425.8X	0.0X	69324.0X	16702.9Mb	39227450	42X	98%	84.3%	0.35%	0.0M	2165.2M	100.0%	97.2%	4.4%	2165.2M	240.3bp
T21-D0003376_S6_L001																							34.3%	97.4%	38812.1Mb	269.8M	52.4%	99.1%	11.4%	150.0bp	150.0bp
T21-D0003376_S6_L002																							32.6%	97.5%	38885.9Mb	269.9M	52.4%	99.1%	11.2%	150.0bp	150.0bp
T21-D0003376_S6_L003																							31.2%	97.3%	39114.4Mb	272.0M	52.5%	99.1%	11.6%	150.0bp	150.0bp
T21-D0003376_S6_L004																							35.3%	97.4%	39288.4Mb	272.9M	52.5%	99.1%	11.4%	150.0bp	150.0bp
T21-D0003376_S6_L005																							34.7%	97.4%	38684.4Mb	268.7M	52.4%	99.1%	11.5%	150.0bp	150.0bp
T21-D0003376_S6_L006																							33.9%	97.4%	38901.4Mb	270.3M	52.4%	99.1%	11.8%	150.0bp	150.0bp
T21-D0003376_S6_L007																							34.2%	97.4%	38961.8Mb	270.7M	52.5%	99.1%	11.7%	150.0bp	150.0bp
T21-D0003376_S6_L008																							34.1%	97.4%	38992.7Mb	270.9M	52.5%	99.1%	11.7%	150.0bp	150.0bp

Expand table

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

Sort	Group	Column	Description	ID	Scale
\|\|	Mosdepth	≥ 1X	Fraction of genome with at least 1X coverage	`mosdepth-1_x_pc`
\|\|	Mosdepth	≥ 5X	Fraction of genome with at least 5X coverage	`mosdepth-5_x_pc`
\|\|	Mosdepth	≥ 10X	Fraction of genome with at least 10X coverage	`mosdepth-10_x_pc`
\|\|	Mosdepth	≥ 30X	Fraction of genome with at least 30X coverage	`mosdepth-30_x_pc`
\|\|	Mosdepth	≥ 50X	Fraction of genome with at least 50X coverage	`mosdepth-50_x_pc`
\|\|	Mosdepth	Median	Median coverage	`mosdepth-median_coverage`
\|\|	Mosdepth	Mean Cov.	Mean coverage	`mosdepth-mean_coverage`
\|\|	Mosdepth	Min Cov.	Minimum coverage	`mosdepth-min_coverage`
\|\|	Mosdepth	Max Cov.	Maximum coverage	`mosdepth-max_coverage`
\|\|	Mosdepth	Mb Total Coverage Bases	Total coverage of bases (millions)	`mosdepth-coverage_bases`	base_count
\|\|	Mosdepth	Genome length	Total length of the genome	`mosdepth-length`
\|\|	Picard: HsMetrics	Fold Enrichment	Fold Enrichment	`picard_hsmetrics-FOLD_ENRICHMENT`
\|\|	Picard: HsMetrics	Target Bases ≥ 30X	Percent of target bases with coverage ≥ 30X	`picard_hsmetrics-picard_target_bases_30X`
\|\|	Picard: Mark Duplicates	Duplication	Mark Duplicates - Percent Duplication	`picard_mark_duplicates-PERCENT_DUPLICATION`
\|\|	Samtools: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_stats-error_rate`
\|\|	Samtools: stats	Non-primary	Non-primary alignments (millions)	`samtools_stats-non_primary_alignments`	read_count
\|\|	Samtools: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_stats-reads_mapped`	read_count
\|\|	Samtools: stats	% Mapped	% Mapped reads	`samtools_stats-reads_mapped_percent`
\|\|	Samtools: stats	% Proper pairs	% Properly paired reads	`samtools_stats-reads_properly_paired_percent`
\|\|	Samtools: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_stats-reads_MQ0_percent`
\|\|	Samtools: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_stats-raw_total_sequences`	read_count
\|\|	Samtools: stats	Mean insert	Average insert size	`samtools_stats-insert_size_average`
\|\|	fastp	% Duplication	Duplication rate before filtering	`fastp-pct_duplication`
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`fastp-after_filtering_q30_rate`
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`fastp-after_filtering_q30_bases`	base_count
\|\|	fastp	Reads After Filtering	Total reads after filtering (millions)	`fastp-filtering_result_passed_filter_reads`	read_count
\|\|	fastp	GC content	GC content after filtering	`fastp-after_filtering_gc_content`
\|\|	fastp	% PF	Percent reads passing filter	`fastp-pct_surviving`
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`fastp-pct_adapter`
\|\|	fastp	Mean R1 Length	Mean read length of R1	`fastp-before_filtering_read1_mean_length`
\|\|	fastp	Mean R2 Length	Mean read length of R2	`fastp-before_filtering_read2_mean_length`

Mosdepth

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.https://github.com/brentp/mosdepthDOI: 10.1093/bioinformatics/btx699

Cumulative coverage distribution

Proportion of bases in the reference genome with, at least, a given depth of coverage. Note that for 32 samples, a BED file was provided, so the data was calculated across those regions. For 32 samples, it's calculated across the entire genome length. 32 samples have both global and region reports, and we are showing the data for regions

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

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

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

Created with MultiQC

Average coverage per contig

Average coverage per contig or chromosome

Created with MultiQC

XY coverage

Created with MultiQC

Picard

Tools for manipulating high-throughput sequencing data.http://broadinstitute.github.io/picard

Hybrid-selection metrics

Parsed from Picard HsMetrics tool that takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection. Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments such as exome sequencing.

Hybrid selection metrics from Sentieon (Picard format)

Showing ³²/₃₂ rows and ¹⁹/₂₄ columns.

Sample Name	At dropout	Bait design efficiency	Bait territory	Fold 80 base penalty	Fold enrichment	Gc dropout	Near-bait bases	Off-bait bases	On-bait bases	On-target bases	Usable bases on-bait	Usable bases on-target	PF bases aligned	PF reads	Selected bases	PF unique reads	PF unique bases aligned	PF unique reads aligned	Total reads	Mean bait coverage	Mean target coverage	On-bait vs selected	Target territory	Zero coverage targets
Filler-D0000335	8.0	0.8	47358034.0	1.6	41.8	0.0	86343.4Mb	43848.4Mb	207980.2Mb	18689.9Mb	61.7%	5.5%	338172.0Mb	2274.3M	87.0%	372.2M	57136.7Mb	372.1M	2274.3M	4391.7	476.4	0.7	39227450.0	0.6%
Filler-D0000539	6.5	0.8	47358034.0	1.5	41.1	0.0	103782.9Mb	51659.5Mb	238469.6Mb	17676.6Mb	60.7%	4.5%	393912.0Mb	2650.2M	86.9%	357.5M	55093.8Mb	357.4M	2650.2M	5035.5	450.6	0.7	39227450.0	0.6%
Filler-D0000637	7.6	0.8	47358034.0	1.6	40.0	0.0	85434.0Mb	40466.5Mb	179804.9Mb	15603.8Mb	59.0%	5.1%	305705.5Mb	2054.4M	86.8%	317.3M	48944.9Mb	317.2M	2054.4M	3796.7	397.8	0.7	39227450.0	0.7%
Filler-D0000789	8.8	0.8	47358034.0	1.6	40.4	0.0	87844.0Mb	42224.1Mb	190674.0Mb	20541.9Mb	59.6%	6.4%	320742.1Mb	2154.8M	86.8%	403.7M	61584.2Mb	403.7M	2154.8M	4026.2	523.6	0.7	39227450.0	0.7%
Filler-D0000861	8.5	0.8	47358034.0	1.7	40.6	0.0	41778.6Mb	20125.6Mb	91770.3Mb	11761.3Mb	59.9%	7.7%	153674.5Mb	1031.0M	86.9%	226.6M	34689.3Mb	226.6M	1031.0M	1937.8	299.8	0.7	39227450.0	0.7%
Filler-D0000890	4.7	0.8	47358034.0	1.4	40.0	0.1	64796.9Mb	32281.9Mb	139178.6Mb	9968.4Mb	59.2%	4.2%	236257.4Mb	1586.3M	86.3%	215.2M	33693.5Mb	215.1M	1586.3M	2938.9	254.1	0.7	39227450.0	0.7%
Filler-D0001009	6.9	0.8	47358034.0	1.5	36.3	0.0	86787.1Mb	39660.3Mb	144924.6Mb	13025.2Mb	53.5%	4.8%	271372.0Mb	1819.4M	85.4%	275.3M	42422.0Mb	275.3M	1819.4M	3060.2	332.0	0.6	39227450.0	0.6%
Filler-D0001089	5.7	0.8	47358034.0	1.5	42.5	0.2	75588.9Mb	40846.6Mb	194831.1Mb	18365.1Mb	62.8%	5.9%	311266.6Mb	2089.8M	86.9%	378.1M	58268.7Mb	378.0M	2089.8M	4114.0	468.2	0.7	39227450.0	0.9%
Filler-D0001104	4.7	0.8	47358034.0	1.4	39.7	0.1	66782.9Mb	32396.4Mb	139829.3Mb	12536.2Mb	58.8%	5.3%	239008.5Mb	1602.4M	86.4%	260.5M	40467.6Mb	260.4M	1602.4M	2952.6	319.6	0.7	39227450.0	0.7%
Filler-D0001215	5.3	0.8	47358034.0	1.5	40.4	0.1	90790.2Mb	45253.6Mb	199089.1Mb	13999.5Mb	59.6%	4.2%	335132.9Mb	2255.3M	86.5%	288.9M	44764.2Mb	288.9M	2255.3M	4203.9	356.9	0.7	39227450.0	0.7%
Filler-D0001322	6.7	0.8	47358034.0	1.5	38.7	0.0	88380.6Mb	41542.6Mb	172366.7Mb	15751.3Mb	57.1%	5.2%	302289.9Mb	2028.6M	86.3%	322.6M	49408.2Mb	322.5M	2028.6M	3639.7	401.5	0.7	39227450.0	0.7%
Filler-D0001361	8.2	0.8	47358034.0	1.7	39.7	0.0	41134.4Mb	19945.0Mb	85668.1Mb	11623.5Mb	58.6%	7.9%	146747.6Mb	986.1M	86.4%	224.8M	34244.9Mb	224.8M	986.1M	1809.0	296.3	0.7	39227450.0	0.6%
Filler-D0001515	5.0	0.8	47358034.0	1.5	38.5	0.1	97509.2Mb	48184.3Mb	190602.7Mb	13901.2Mb	56.8%	4.1%	336296.3Mb	2260.7M	85.7%	294.0M	45637.6Mb	293.9M	2260.7M	4024.7	354.4	0.7	39227450.0	0.6%
Filler-D0002474	5.3	0.8	47358034.0	1.5	39.1	0.1	94424.7Mb	43754.1Mb	187003.1Mb	14182.5Mb	57.6%	4.4%	325181.9Mb	2185.9M	86.5%	295.7M	45249.8Mb	295.6M	2185.9M	3948.7	361.5	0.7	39227450.0	0.7%
Filler-D0002530	8.7	0.8	47358034.0	1.6	42.0	0.0	86993.9Mb	43368.0Mb	210855.1Mb	18499.7Mb	61.9%	5.4%	341217.1Mb	2302.2M	87.3%	370.2M	56136.8Mb	370.1M	2302.2M	4452.4	471.6	0.7	39227450.0	0.7%
Filler-D0002564	5.1	0.8	47358034.0	1.4	37.4	0.1	78475.9Mb	38088.6Mb	143007.9Mb	11100.3Mb	55.3%	4.3%	259572.4Mb	1741.1M	85.3%	241.5M	37749.2Mb	241.4M	1741.1M	3019.7	283.0	0.6	39227450.0	0.7%
Filler-D0002693	4.7	0.8	47358034.0	1.4	37.6	0.2	112393.5Mb	52475.8Mb	204913.2Mb	12814.0Mb	55.6%	3.5%	369782.5Mb	2481.0M	85.8%	275.1M	43079.3Mb	275.0M	2481.0M	4326.9	326.6	0.6	39227450.0	0.6%
Filler-D0002805	3.7	0.8	47358034.0	1.4	37.7	0.4	80419.4Mb	38683.0Mb	148893.6Mb	10318.9Mb	55.8%	3.9%	267996.0Mb	1795.2M	85.6%	229.2M	35840.1Mb	229.1M	1795.2M	3144.0	263.1	0.6	39227450.0	0.7%
Filler-D0002881	6.0	0.8	47358034.0	1.5	41.2	0.0	63813.5Mb	32523.9Mb	148695.2Mb	15598.7Mb	60.8%	6.4%	245032.6Mb	1651.9M	86.7%	313.6M	47522.3Mb	313.6M	1651.9M	3139.8	397.6	0.7	39227450.0	0.6%
Filler-D0002923	6.9	0.8	47358034.0	1.5	39.8	0.0	66011.3Mb	32862.7Mb	140235.1Mb	14666.2Mb	58.9%	6.2%	239109.1Mb	1602.4M	86.3%	298.4M	46040.0Mb	298.4M	1602.4M	2961.2	373.9	0.7	39227450.0	0.7%
Filler-D0002999	8.6	0.8	47358034.0	1.6	42.6	0.0	104171.5Mb	54624.0Mb	266276.1Mb	18812.8Mb	62.8%	4.4%	425071.6Mb	2880.9M	87.1%	375.5M	57825.4Mb	375.4M	2880.9M	5622.6	479.5	0.7	39227450.0	0.7%
Filler-D0003090	10.9	0.8	47358034.0	1.6	40.8	0.0	76030.3Mb	37023.4Mb	169723.5Mb	17519.8Mb	60.2%	6.2%	282777.2Mb	1907.0M	86.9%	347.5M	53097.1Mb	347.4M	1907.0M	3583.8	446.6	0.7	39227450.0	0.7%
Filler-D0003105	8.1	0.8	47358034.0	1.5	40.5	0.0	75038.4Mb	36614.9Mb	164547.0Mb	13725.4Mb	59.7%	5.0%	276200.3Mb	1858.5M	86.7%	283.5M	43456.8Mb	283.5M	1858.5M	3474.5	349.9	0.7	39227450.0	0.7%
Filler-D0003157	9.5	0.8	47358034.0	1.7	39.9	0.0	73938.4Mb	35592.6Mb	156064.5Mb	19132.8Mb	59.0%	7.2%	265595.5Mb	1777.9M	86.6%	376.8M	57873.8Mb	376.7M	1777.9M	3295.4	487.7	0.7	39227450.0	0.6%
Filler-D0003224	10.1	0.8	47358034.0	1.6	40.3	0.0	76887.6Mb	36384.1Mb	165236.3Mb	15185.0Mb	59.5%	5.5%	278508.0Mb	1877.3M	86.9%	308.6M	47096.9Mb	308.5M	1877.3M	3489.1	387.1	0.7	39227450.0	0.6%
Filler-D0003241	10.2	0.8	47358034.0	1.6	40.9	0.0	71661.4Mb	35441.9Mb	161636.6Mb	16172.6Mb	60.4%	6.0%	268740.0Mb	1810.1M	86.8%	322.9M	49466.3Mb	322.8M	1810.1M	3413.1	412.3	0.7	39227450.0	0.6%
Filler-D0003441	6.0	0.8	47358034.0	1.4	40.4	0.0	98373.4Mb	48342.9Mb	215475.7Mb	13120.3Mb	59.7%	3.6%	362192.0Mb	2437.5M	86.7%	278.4M	43462.9Mb	278.3M	2437.5M	4549.9	334.5	0.7	39227450.0	0.7%
T13-D0003360	9.4	0.8	47358034.0	1.5	40.4	0.0	108380.9Mb	49490.8Mb	231406.8Mb	12678.9Mb	59.6%	3.3%	389278.4Mb	2627.5M	87.3%	269.2M	41687.2Mb	269.1M	2627.5M	4886.3	323.2	0.7	39227450.0	0.6%
T18-D0001467	4.5	0.8	47358034.0	1.6	34.3	0.3	94250.2Mb	47176.0Mb	144510.6Mb	14982.0Mb	50.7%	5.3%	285936.8Mb	1909.4M	83.5%	319.9M	49719.5Mb	319.8M	1909.4M	3051.4	381.8	0.6	39227450.0	0.5%
T18-D0003255	9.2	0.8	47358034.0	1.6	39.3	0.0	119195.1Mb	54576.9Mb	238300.7Mb	15515.4Mb	58.0%	3.8%	412072.7Mb	2768.0M	86.8%	323.7M	50144.6Mb	323.7M	2768.0M	5031.9	395.5	0.7	39227450.0	0.7%
T21-D0003322	9.2	0.8	47358034.0	1.6	40.1	0.0	83935.6Mb	39653.1Mb	177799.2Mb	14531.6Mb	59.2%	4.8%	301387.9Mb	2026.4M	86.8%	296.6M	45959.0Mb	296.5M	2026.4M	3754.4	370.4	0.7	39227450.0	0.6%
T21-D0003376	9.9	0.8	47358034.0	1.6	41.5	0.0	83845.9Mb	40723.7Mb	196146.6Mb	17148.1Mb	61.3%	5.4%	320716.1Mb	2165.2M	87.3%	339.2M	51751.0Mb	339.1M	2165.2M	4141.8	437.1	0.7	39227450.0	0.7%

Expand table

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

Sort	Column	Description	ID	Scale
\|\|	At dropout	A measure of how undercovered <= 50% GC regions are relative to the mean.	`hsmetrics-AT_DROPOUT`
\|\|	Bait design efficiency	Target territory / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target.	`hsmetrics-BAIT_DESIGN_EFFICIENCY`
\|\|	Bait territory	The number of bases which have one or more baits on top of them.	`hsmetrics-BAIT_TERRITORY`
\|\|	Fold 80 base penalty	The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.	`hsmetrics-FOLD_80_BASE_PENALTY`
\|\|	Fold enrichment	The fold by which the baited region has been amplified above genomic background.	`hsmetrics-FOLD_ENRICHMENT`
\|\|	Gc dropout	A measure of how undercovered >= 50% GC regions are relative to the mean.	`hsmetrics-GC_DROPOUT`
\|\|	Near-bait bases	The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.	`hsmetrics-NEAR_BAIT_BASES`	base_count
\|\|	Off-bait bases	The number of PF aligned bases that mapped to neither on or near a bait.	`hsmetrics-OFF_BAIT_BASES`	base_count
\|\|	On-bait bases	The number of PF aligned bases that mapped to a baited region of the genome.	`hsmetrics-ON_BAIT_BASES`	base_count
\|\|	On-target bases	The number of PF aligned bases that mapped to a targeted region of the genome.	`hsmetrics-ON_TARGET_BASES`	base_count
\|\|	Usable bases on-bait	The number of aligned, de-duped, on-bait bases out of the PF bases available.	`hsmetrics-PCT_USABLE_BASES_ON_BAIT`
\|\|	Usable bases on-target	The number of aligned, de-duped, on-target bases out of the PF bases available.	`hsmetrics-PCT_USABLE_BASES_ON_TARGET`
\|\|	PF bases aligned	The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.	`hsmetrics-PF_BASES_ALIGNED`	base_count
\|\|	PF reads	The number of reads that pass the vendor's filter.	`hsmetrics-PF_READS`	read_count
\|\|	Selected bases	On+Near Bait Bases / PF Bases Aligned.	`hsmetrics-PCT_SELECTED_BASES`
\|\|	PF unique reads	The number of PF reads that are not marked as duplicates.	`hsmetrics-PF_UNIQUE_READS`	read_count
\|\|	PF unique bases aligned	The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps.	`hsmetrics-PF_UQ_BASES_ALIGNED`	base_count
\|\|	PF unique reads aligned	The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.	`hsmetrics-PF_UQ_READS_ALIGNED`	read_count
\|\|	Total reads	The total number of reads in the SAM or BAM file examine.	`hsmetrics-TOTAL_READS`	read_count
\|\|	Mean bait coverage	The mean coverage of all baits in the experiment.	`hsmetrics-MEAN_BAIT_COVERAGE`
\|\|	Mean target coverage	The mean coverage of targets.	`hsmetrics-MEAN_TARGET_COVERAGE`
\|\|	On-bait vs selected	The percentage of on+near bait bases that are on as opposed to near.	`hsmetrics-ON_BAIT_VS_SELECTED`
\|\|	Target territory	The unique number of target bases in the experiment where target is usually exons etc.	`hsmetrics-TARGET_TERRITORY`
\|\|	Zero coverage targets	The fraction of targets that did not reach coverage=1 over any base.	`hsmetrics-ZERO_CVG_TARGETS_PCT`

Hybrid-selection target coverage

The percentage of all target bases with at least x fold coverage.

Created with MultiQC

Hybrid-selection penalty

The "hybrid selection penalty" incurred to get 80% of target bases to a given coverage.

Can be used with the following formula:

required_aligned_bases = bait_size_bp * desired_coverage * hs_penalty

Created with MultiQC

Mark Duplicates

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

Duplicate marking metrics from Sentieon MarkDuplicates

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

Created with MultiQC

Samtools

Version:


                      
                        1.21

HTSlib:


                      
                        1.23

Toolkit for interacting with BAM/CRAM files.http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Percent mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

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).

Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

Created with MultiQC

Alignment stats

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

Alignment statistics from samtools stats on post-dedup BAMs

Created with MultiQC

Showing ³²/₃₂ rows and ¹³/₁₃ columns.

Sample Name	Total sequences	Mapped & paired	Properly paired	Duplicated	QC Failed	Reads MQ0	Mapped bases (CIGAR)	Bases Trimmed	Duplicated bases	Diff chromosomes	Other orientation	Inward pairs	Outward pairs
Filler-D0000335	2274.3M	2274.2M	2200.9M	1902.1M	0.0M	102.2M	338328.8Mb	0.0Mb	282045.2Mb	21.0M	0.9M	1053.8M	61.4M
Filler-D0000539	2650.2M	2650.1M	2577.2M	2292.7M	0.0M	110.3M	394100.8Mb	0.0Mb	340083.9Mb	25.8M	1.0M	1232.9M	65.3M
Filler-D0000637	2054.4M	2054.3M	1996.7M	1737.1M	0.0M	89.6M	305840.4Mb	0.0Mb	257675.2Mb	23.1M	0.9M	958.1M	45.1M
Filler-D0000789	2154.8M	2154.7M	2098.1M	1751.1M	0.0M	94.9M	320877.4Mb	0.0Mb	260081.7Mb	22.2M	0.8M	1009.1M	45.3M
Filler-D0000861	1031.0M	1030.9M	1006.9M	804.3M	0.0M	43.4M	153740.1Mb	0.0Mb	119445.9Mb	9.2M	0.3M	482.7M	23.2M
Filler-D0000890	1586.3M	1586.3M	1537.6M	1371.2M	0.0M	66.7M	236352.0Mb	0.0Mb	203299.8Mb	19.5M	0.7M	735.9M	37.0M
Filler-D0001009	1819.4M	1819.3M	1760.4M	1544.1M	0.0M	74.8M	271479.2Mb	0.0Mb	229770.2Mb	27.0M	0.9M	854.2M	27.5M
Filler-D0001089	2089.8M	2089.7M	1858.4M	1711.7M	0.0M	98.8M	311417.4Mb	0.0Mb	253978.9Mb	17.7M	2.0M	973.4M	51.7M
Filler-D0001104	1602.4M	1602.3M	1562.1M	1342.0M	0.0M	61.8M	239109.9Mb	0.0Mb	199306.4Mb	16.0M	0.6M	750.5M	34.1M
Filler-D0001215	2255.3M	2255.2M	2189.3M	1966.4M	0.0M	95.5M	335287.3Mb	0.0Mb	291411.7Mb	25.0M	1.0M	1046.0M	55.6M
Filler-D0001322	2028.6M	2028.5M	1972.0M	1706.1M	0.0M	85.5M	302409.1Mb	0.0Mb	253763.1Mb	24.3M	0.9M	952.6M	36.5M
Filler-D0001361	986.1M	986.1M	959.0M	761.3M	0.0M	43.2M	146813.7Mb	0.0Mb	112940.6Mb	11.2M	0.4M	457.3M	24.2M
Filler-D0001515	2260.7M	2260.6M	2187.6M	1966.7M	0.0M	94.7M	336430.2Mb	0.0Mb	291718.0Mb	32.0M	1.2M	1049.7M	47.5M
Filler-D0002474	2185.9M	2185.7M	2129.9M	1890.2M	0.0M	86.9M	325313.3Mb	0.0Mb	280890.4Mb	24.0M	0.9M	1027.2M	40.9M
Filler-D0002530	2302.2M	2302.1M	2218.4M	1932.0M	0.0M	104.5M	341355.0Mb	0.0Mb	286027.4Mb	20.0M	1.0M	1066.9M	63.1M
Filler-D0002564	1741.1M	1741.0M	1685.0M	1499.6M	0.0M	72.7M	259675.2Mb	0.0Mb	222671.5Mb	25.3M	0.9M	811.7M	32.7M
Filler-D0002693	2481.0M	2480.9M	2406.1M	2205.9M	0.0M	96.7M	369924.3Mb	0.0Mb	327832.2Mb	33.5M	1.2M	1159.7M	46.1M
Filler-D0002805	1795.2M	1795.2M	1742.2M	1566.1M	0.0M	74.2M	268100.9Mb	0.0Mb	232973.9Mb	23.6M	0.8M	843.0M	30.2M
Filler-D0002881	1651.9M	1651.7M	1607.5M	1338.2M	0.0M	72.3M	245144.5Mb	0.0Mb	198248.5Mb	15.2M	0.6M	766.9M	43.2M
Filler-D0002923	1602.4M	1602.3M	1556.8M	1304.0M	0.0M	67.1M	239207.5Mb	0.0Mb	193790.2Mb	18.0M	0.7M	749.1M	33.4M
Filler-D0002999	2880.9M	2880.7M	2692.4M	2505.4M	0.0M	135.2M	425247.0Mb	0.0Mb	368554.4Mb	26.8M	1.8M	1302.8M	108.9M
Filler-D0003090	1907.0M	1906.9M	1859.1M	1559.6M	0.0M	84.3M	282897.4Mb	0.0Mb	230529.7Mb	18.0M	0.7M	880.5M	54.3M
Filler-D0003105	1858.5M	1858.4M	1808.8M	1575.0M	0.0M	79.2M	276324.3Mb	0.0Mb	233589.8Mb	18.9M	0.7M	863.7M	45.9M
Filler-D0003157	1777.9M	1777.8M	1728.3M	1401.2M	0.0M	77.6M	265707.4Mb	0.0Mb	208517.3Mb	19.8M	0.7M	837.1M	31.3M
Filler-D0003224	1877.3M	1877.2M	1823.6M	1568.7M	0.0M	82.1M	278619.2Mb	0.0Mb	232199.1Mb	21.3M	0.8M	867.4M	49.1M
Filler-D0003241	1810.1M	1810.0M	1760.8M	1487.3M	0.0M	78.1M	268862.3Mb	0.0Mb	220115.9Mb	17.8M	0.7M	836.5M	50.0M
Filler-D0003441	2437.5M	2437.4M	2361.1M	2159.2M	0.0M	101.3M	362337.6Mb	0.0Mb	319813.7Mb	28.9M	1.1M	1131.6M	57.1M
T13-D0003360	2627.5M	2627.3M	2565.1M	2358.2M	0.0M	112.8M	389426.7Mb	0.0Mb	348727.0Mb	24.7M	0.9M	1214.3M	73.8M
T18-D0001467	1909.4M	1909.3M	1821.9M	1589.5M	0.0M	77.1M	286037.2Mb	0.0Mb	237091.5Mb	40.4M	1.4M	893.2M	19.7M
T18-D0003255	2768.0M	2767.9M	2683.9M	2444.3M	0.0M	114.4M	412230.6Mb	0.0Mb	363120.2Mb	35.3M	1.3M	1292.9M	54.4M
T21-D0003322	2026.4M	2026.3M	1966.2M	1729.8M	0.0M	84.0M	301501.0Mb	0.0Mb	256314.2Mb	24.2M	0.9M	938.7M	49.3M
T21-D0003376	2165.2M	2165.1M	2105.0M	1826.1M	0.0M	94.6M	320844.2Mb	0.0Mb	269886.8Mb	20.5M	0.8M	994.8M	66.5M

Expand table

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-stats-dp_table

Sort	Column	Description	ID	Scale
\|\|	Total sequences	Total sequences	`raw_total_sequences`	read_count
\|\|	Mapped & paired	Paired-end technology bit set + both mates mapped	`reads_mapped_and_paired`	read_count
\|\|	Properly paired	Proper-pair bit set	`reads_properly_paired`	read_count
\|\|	Duplicated	PCR or optical duplicate bit set	`reads_duplicated`	read_count
\|\|	QC Failed	QC Failed	`reads_QC_failed`	read_count
\|\|	Reads MQ0	Reads mapped and MQ=0	`reads_MQ0`	read_count
\|\|	Mapped bases (CIGAR)	Mapped bases (CIGAR)	`bases_mapped__cigar`	base_count
\|\|	Bases Trimmed	Bases Trimmed	`bases_trimmed`	base_count
\|\|	Duplicated bases	Duplicated bases	`bases_duplicated`	base_count
\|\|	Diff chromosomes	Pairs on different chromosomes	`pairs_on_different_chromosomes`	read_count
\|\|	Other orientation	Pairs with other orientation	`pairs_with_other_orientation`	read_count
\|\|	Inward pairs	Inward oriented pairs	`inward_oriented_pairs`	read_count
\|\|	Outward pairs	Outward oriented pairs	`outward_oriented_pairs`	read_count

fastp

Version:


                      
                        1.0.1

All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

Pre-alignment QC and adapter trimming, run per sample

Filtered Reads

Filtering statistics of sampled reads.

Created with MultiQC

Insert Sizes

Insert size estimation of sampled reads.

Created with MultiQC

Sequence Quality

Average sequencing quality over each base of all reads.

Created with MultiQC

GC Content

Average GC content over each base of all reads.

Created with MultiQC

N content

Average N content over each base of all reads.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Group	Software	Version
Samtools	HTSlib	`1.23`
	Samtools	`1.21`
fastp	fastp	`1.0.1`

20260603_LH00166_0309_A23WCJNLT4

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20260603_LH00166_0309_A23WCJNLT4

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General Statistics

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General Statistics: Columns

Mosdepth

Cumulative coverage distribution Help

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Average coverage per contig

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XY coverage

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Picard

Hybrid-selection metrics

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Picard HsMetrics: Columns

Hybrid-selection target coverage

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Hybrid-selection penalty Help

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Mark Duplicates Help

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Samtools

Percent mapped Help

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Alignment stats

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Samtools: stats: Alignment Stats: Columns

fastp

Filtered Reads

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Insert Sizes

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Sequence Quality

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GC Content

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