20260529_LH00995_0049_B23YT2HLT4

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

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Report generated on 2026-06-06, 21:59 UTC based on data in: /tmp/nxf.D4aDEhlybU

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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
1_25PercentHG514	100.0%	100.0%	100.0%	100.0%	100.0%	1359X	1461.9X	0.0X	134104.0X	57345.3Mb	39227450	38X	99%	75.4%	0.29%	0.0M	4786.5M	100.0%	98.5%	4.5%	4786.7M	269.4bp
1_25PercentHG514_S7_L001																							29.5%	97.6%	79642.2Mb	595.9M	49.5%	99.2%	19.1%	150.0bp	150.0bp
1_25PercentHG514_S7_L002																							29.9%	97.6%	79976.4Mb	597.8M	49.6%	99.2%	18.8%	150.0bp	150.0bp
1_25PercentHG514_S7_L003																							29.4%	97.5%	79540.4Mb	595.6M	49.6%	99.2%	19.1%	150.0bp	150.0bp
1_25PercentHG514_S7_L004																							29.0%	97.5%	78759.2Mb	590.2M	49.6%	99.2%	19.2%	150.0bp	150.0bp
1_25PercentHG514_S7_L005																							30.2%	97.5%	79681.4Mb	595.7M	49.6%	99.2%	18.6%	150.0bp	150.0bp
1_25PercentHG514_S7_L006																							29.5%	97.5%	79805.0Mb	597.8M	49.7%	99.1%	19.1%	150.0bp	150.0bp
1_25PercentHG514_S7_L007																							30.7%	97.6%	80837.9Mb	604.1M	49.6%	99.2%	18.6%	150.0bp	150.0bp
1_25PercentHG514_S7_L008																							31.4%	97.7%	81717.2Mb	609.7M	49.5%	99.2%	18.3%	150.0bp	150.0bp
1_25PercentNA24385	100.0%	100.0%	100.0%	100.0%	100.0%	579X	655.9X	0.0X	91864.0X	25728.0Mb	39227450	38X	99%	69.2%	0.27%	0.0M	1644.9M	100.0%	98.6%	4.5%	1644.9M	263.7bp
1_25PercentNA24385_S15_L001																							24.7%	97.6%	27345.8Mb	205.0M	49.4%	99.2%	19.9%	150.0bp	150.0bp
1_25PercentNA24385_S15_L002																							25.1%	97.6%	27416.8Mb	205.4M	49.5%	99.2%	19.7%	150.0bp	150.0bp
1_25PercentNA24385_S15_L003																							24.6%	97.5%	27290.8Mb	204.8M	49.5%	99.2%	20.0%	150.0bp	150.0bp
1_25PercentNA24385_S15_L004																							24.1%	97.5%	27008.4Mb	202.9M	49.5%	99.2%	20.1%	150.0bp	150.0bp
1_25PercentNA24385_S15_L005																							25.3%	97.6%	27273.0Mb	204.4M	49.5%	99.2%	19.6%	150.0bp	150.0bp
1_25PercentNA24385_S15_L006																							24.6%	97.5%	27351.2Mb	205.3M	49.5%	99.2%	20.0%	150.0bp	150.0bp
1_25PercentNA24385_S15_L007																							25.8%	97.6%	27685.1Mb	207.4M	49.5%	99.2%	19.5%	150.0bp	150.0bp
1_25PercentNA24385_S15_L008																							26.5%	97.7%	28060.4Mb	209.8M	49.4%	99.3%	19.3%	150.0bp	150.0bp
2_5PercentHG514	100.0%	100.0%	100.0%	100.0%	100.0%	1363X	1463.5X	0.0X	127373.0X	57410.1Mb	39227450	38X	99%	75.3%	0.28%	0.0M	4777.5M	100.0%	98.5%	4.5%	4777.6M	272.2bp
2_5PercentHG514_S6_L001																							28.6%	97.5%	79761.8Mb	597.0M	49.5%	99.2%	18.8%	150.0bp	150.0bp
2_5PercentHG514_S6_L002																							28.9%	97.5%	79750.6Mb	596.5M	49.6%	99.2%	18.7%	150.0bp	150.0bp
2_5PercentHG514_S6_L003																							28.3%	97.4%	79353.3Mb	594.6M	49.7%	99.2%	18.9%	150.0bp	150.0bp
2_5PercentHG514_S6_L004																							27.9%	97.4%	78494.6Mb	588.7M	49.6%	99.2%	19.1%	150.0bp	150.0bp
2_5PercentHG514_S6_L005																							29.0%	97.4%	79022.5Mb	591.4M	49.7%	99.2%	18.5%	150.0bp	150.0bp
2_5PercentHG514_S6_L006																							28.4%	97.4%	79433.6Mb	595.4M	49.7%	99.2%	19.0%	150.0bp	150.0bp
2_5PercentHG514_S6_L007																							29.6%	97.5%	80637.7Mb	603.0M	49.6%	99.2%	18.4%	150.0bp	150.0bp
2_5PercentHG514_S6_L008																							30.4%	97.6%	81871.8Mb	611.1M	49.5%	99.2%	18.2%	150.0bp	150.0bp
2_5PercentNA24385	100.0%	100.0%	100.0%	100.0%	100.0%	1288X	1391.2X	0.0X	131838.0X	54574.9Mb	39227450	38X	99%	68.1%	0.28%	0.0M	3476.3M	100.0%	98.5%	4.5%	3476.4M	271.7bp
2_5PercentNA24385_S14_L001																							26.0%	97.6%	58087.0Mb	433.8M	49.5%	99.2%	18.4%	150.0bp	150.0bp
2_5PercentNA24385_S14_L002																							26.5%	97.6%	58373.2Mb	435.6M	49.6%	99.2%	18.2%	150.0bp	150.0bp
2_5PercentNA24385_S14_L003																							25.9%	97.5%	57764.0Mb	431.9M	49.7%	99.2%	18.5%	150.0bp	150.0bp
2_5PercentNA24385_S14_L004																							25.5%	97.5%	57386.3Mb	429.4M	49.7%	99.2%	18.6%	150.0bp	150.0bp
2_5PercentNA24385_S14_L005																							26.8%	97.5%	58019.8Mb	433.2M	49.7%	99.2%	18.1%	150.0bp	150.0bp
2_5PercentNA24385_S14_L006																							25.9%	97.5%	57752.0Mb	432.0M	49.7%	99.2%	18.6%	150.0bp	150.0bp
2_5PercentNA24385_S14_L007																							27.2%	97.6%	58848.0Mb	439.2M	49.6%	99.2%	18.1%	150.0bp	150.0bp
2_5PercentNA24385_S14_L008																							28.0%	97.7%	59229.1Mb	441.3M	49.6%	99.2%	17.8%	150.0bp	150.0bp
5PercentHG514	100.0%	100.0%	100.0%	100.0%	100.0%	624X	700.8X	0.0X	99885.0X	27492.0Mb	39227450	38X	99%	66.1%	0.29%	0.0M	1597.4M	100.0%	98.5%	4.5%	1597.4M	276.1bp
5PercentHG514_S5_L001																							25.8%	97.6%	26481.5Mb	197.6M	49.4%	99.2%	18.2%	150.0bp	150.0bp
5PercentHG514_S5_L002																							26.4%	97.6%	26842.7Mb	200.1M	49.5%	99.2%	17.9%	150.0bp	150.0bp
5PercentHG514_S5_L003																							25.8%	97.5%	26679.9Mb	199.3M	49.5%	99.2%	18.2%	150.0bp	150.0bp
5PercentHG514_S5_L004																							25.3%	97.5%	26500.7Mb	198.1M	49.5%	99.2%	18.3%	150.0bp	150.0bp
5PercentHG514_S5_L005																							26.9%	97.5%	27007.4Mb	201.4M	49.5%	99.2%	17.7%	150.0bp	150.0bp
5PercentHG514_S5_L006																							25.8%	97.5%	26713.6Mb	199.6M	49.5%	99.2%	18.2%	150.0bp	150.0bp
5PercentHG514_S5_L007																							27.2%	97.6%	26994.1Mb	201.2M	49.5%	99.2%	17.8%	150.0bp	150.0bp
5PercentHG514_S5_L008																							27.8%	97.7%	26887.4Mb	200.1M	49.4%	99.2%	17.6%	150.0bp	150.0bp
5PercentNA24385	100.0%	100.0%	100.0%	100.0%	100.0%	1445X	1557.1X	0.0X	139091.0X	61080.1Mb	39227450	37X	99%	73.5%	0.28%	0.0M	4725.0M	100.0%	98.3%	4.5%	4725.1M	278.0bp
5PercentNA24385_S13_L001																							28.6%	97.5%	78781.1Mb	588.6M	49.5%	99.1%	18.1%	150.0bp	150.0bp
5PercentNA24385_S13_L002																							29.0%	97.5%	79340.2Mb	592.3M	49.6%	99.2%	17.9%	150.0bp	150.0bp
5PercentNA24385_S13_L003																							28.4%	97.4%	78607.8Mb	587.8M	49.6%	99.1%	18.1%	150.0bp	150.0bp
5PercentNA24385_S13_L004																							28.0%	97.4%	78081.8Mb	584.4M	49.6%	99.1%	18.2%	150.0bp	150.0bp
5PercentNA24385_S13_L005																							29.2%	97.4%	79235.1Mb	591.7M	49.6%	99.2%	17.7%	150.0bp	150.0bp
5PercentNA24385_S13_L006																							28.4%	97.4%	78552.8Mb	587.7M	49.6%	99.1%	18.2%	150.0bp	150.0bp
5PercentNA24385_S13_L007																							29.6%	97.5%	79568.0Mb	594.0M	49.6%	99.1%	17.7%	150.0bp	150.0bp
5PercentNA24385_S13_L008																							30.3%	97.6%	80322.7Mb	598.6M	49.5%	99.2%	17.5%	150.0bp	150.0bp
10PercentHG514	100.0%	98.0%	85.0%	13.0%	4.0%	17X	20.7X	0.0X	10394.0X	810.7Mb	39227450	36X	15%	66.6%	0.30%	0.0M	45.3M	100.0%	98.1%	4.6%	45.3M	320.7bp
10PercentHG514_S4_L001																							27.4%	97.2%	761.0Mb	5.6M	49.2%	99.1%	14.1%	150.0bp	150.0bp
10PercentHG514_S4_L002																							27.8%	97.2%	764.7Mb	5.7M	49.3%	99.1%	13.9%	150.0bp	150.0bp
10PercentHG514_S4_L003																							27.1%	97.1%	756.9Mb	5.6M	49.3%	99.1%	14.2%	150.0bp	150.0bp
10PercentHG514_S4_L004																							26.5%	97.0%	751.5Mb	5.6M	49.3%	99.0%	14.3%	150.0bp	150.0bp
10PercentHG514_S4_L005																							28.2%	97.0%	765.8Mb	5.7M	49.3%	99.1%	13.7%	150.0bp	150.0bp
10PercentHG514_S4_L006																							27.1%	97.1%	758.3Mb	5.6M	49.4%	99.0%	14.2%	150.0bp	150.0bp
10PercentHG514_S4_L007																							28.5%	97.1%	771.2Mb	5.7M	49.3%	99.1%	13.8%	150.0bp	150.0bp
10PercentHG514_S4_L008																							29.4%	97.2%	783.5Mb	5.8M	49.2%	99.1%	13.6%	150.0bp	150.0bp
10PercentNA24385	100.0%	100.0%	100.0%	100.0%	100.0%	1458X	1570.0X	0.0X	134258.0X	61586.6Mb	39227450	38X	99%	73.1%	0.28%	0.0M	4701.0M	100.0%	98.4%	4.5%	4701.1M	266.2bp
10PercentNA24385_S12_L001																							26.8%	97.5%	77749.1Mb	583.7M	49.4%	99.2%	19.9%	150.0bp	150.0bp
10PercentNA24385_S12_L002																							27.3%	97.5%	78425.6Mb	588.2M	49.5%	99.2%	19.6%	150.0bp	150.0bp
10PercentNA24385_S12_L003																							26.8%	97.4%	77939.0Mb	585.5M	49.5%	99.2%	19.9%	150.0bp	150.0bp
10PercentNA24385_S12_L004																							26.4%	97.4%	77172.8Mb	580.3M	49.5%	99.2%	20.0%	150.0bp	150.0bp
10PercentNA24385_S12_L005																							27.5%	97.5%	78338.8Mb	587.7M	49.5%	99.2%	19.5%	150.0bp	150.0bp
10PercentNA24385_S12_L006																							26.8%	97.4%	78121.7Mb	587.1M	49.5%	99.2%	19.9%	150.0bp	150.0bp
10PercentNA24385_S12_L007																							28.0%	97.5%	79034.8Mb	592.6M	49.5%	99.2%	19.4%	150.0bp	150.0bp
10PercentNA24385_S12_L008																							28.6%	97.6%	79603.4Mb	596.0M	49.4%	99.2%	19.2%	150.0bp	150.0bp
20PercentHG514	100.0%	100.0%	100.0%	100.0%	100.0%	1243X	1333.8X	0.0X	126307.0X	52320.5Mb	39227450	38X	99%	70.1%	0.29%	0.0M	3584.8M	100.0%	98.5%	4.5%	3585.0M	274.8bp
20PercentHG514_S3_L001																							26.4%	97.5%	59970.4Mb	447.5M	49.6%	99.1%	18.0%	150.0bp	150.0bp
20PercentHG514_S3_L002																							26.9%	97.5%	60181.3Mb	448.7M	49.7%	99.2%	17.8%	150.0bp	150.0bp
20PercentHG514_S3_L003																							26.3%	97.4%	59617.6Mb	445.3M	49.8%	99.1%	18.1%	150.0bp	150.0bp
20PercentHG514_S3_L004																							25.9%	97.4%	59077.2Mb	441.6M	49.7%	99.1%	18.2%	150.0bp	150.0bp
20PercentHG514_S3_L005																							27.1%	97.4%	59896.5Mb	446.8M	49.8%	99.2%	17.7%	150.0bp	150.0bp
20PercentHG514_S3_L006																							26.3%	97.4%	59597.0Mb	445.3M	49.8%	99.1%	18.1%	150.0bp	150.0bp
20PercentHG514_S3_L007																							27.6%	97.5%	60792.3Mb	453.3M	49.7%	99.2%	17.6%	150.0bp	150.0bp
20PercentHG514_S3_L008																							28.4%	97.6%	61333.1Mb	456.5M	49.6%	99.2%	17.3%	150.0bp	150.0bp
20PercentNA24385	100.0%	100.0%	100.0%	100.0%	100.0%	1376X	1485.1X	0.0X	139678.0X	58256.2Mb	39227450	38X	99%	70.7%	0.29%	0.0M	4057.4M	100.0%	98.5%	4.5%	4057.7M	265.0bp
20PercentNA24385_S11_L001																							26.8%	97.5%	67144.4Mb	503.1M	49.7%	99.0%	19.5%	150.0bp	150.0bp
20PercentNA24385_S11_L002																							27.4%	97.6%	68040.2Mb	509.3M	49.7%	99.0%	19.2%	150.0bp	150.0bp
20PercentNA24385_S11_L003																							26.8%	97.5%	67511.1Mb	506.3M	49.8%	99.0%	19.5%	150.0bp	150.0bp
20PercentNA24385_S11_L004																							26.4%	97.4%	66998.5Mb	502.8M	49.8%	99.0%	19.6%	150.0bp	150.0bp
20PercentNA24385_S11_L005																							27.7%	97.5%	68058.1Mb	509.5M	49.8%	99.0%	19.0%	150.0bp	150.0bp
20PercentNA24385_S11_L006																							26.8%	97.4%	67451.6Mb	506.0M	49.8%	99.0%	19.5%	150.0bp	150.0bp
20PercentNA24385_S11_L007																							28.1%	97.5%	68288.8Mb	511.1M	49.7%	99.0%	19.0%	150.0bp	150.0bp
20PercentNA24385_S11_L008																							28.7%	97.6%	68187.5Mb	509.5M	49.7%	99.0%	18.8%	150.0bp	150.0bp
40PercentHG514	100.0%	100.0%	100.0%	100.0%	100.0%	794X	875.0X	0.0X	102143.0X	34323.6Mb	39227450	38X	99%	71.7%	0.29%	0.0M	2434.4M	100.0%	98.3%	4.6%	2434.5M	272.2bp
40PercentHG514_S2_L001																							26.4%	97.5%	40772.4Mb	305.1M	49.6%	99.2%	18.8%	150.0bp	150.0bp
40PercentHG514_S2_L002																							26.7%	97.6%	40625.2Mb	303.7M	49.7%	99.2%	18.6%	150.0bp	150.0bp
40PercentHG514_S2_L003																							26.1%	97.5%	40409.9Mb	302.7M	49.8%	99.2%	18.9%	150.0bp	150.0bp
40PercentHG514_S2_L004																							25.7%	97.4%	40022.1Mb	300.0M	49.7%	99.2%	19.0%	150.0bp	150.0bp
40PercentHG514_S2_L005																							26.8%	97.5%	40394.6Mb	302.2M	49.8%	99.2%	18.5%	150.0bp	150.0bp
40PercentHG514_S2_L006																							26.1%	97.4%	40450.0Mb	303.1M	49.8%	99.2%	18.9%	150.0bp	150.0bp
40PercentHG514_S2_L007																							27.4%	97.5%	41032.8Mb	306.8M	49.7%	99.2%	18.4%	150.0bp	150.0bp
40PercentHG514_S2_L008																							28.1%	97.6%	41663.8Mb	310.9M	49.6%	99.2%	18.1%	150.0bp	150.0bp
40PercentNA24385	100.0%	100.0%	100.0%	100.0%	100.0%	333X	385.6X	0.0X	77329.0X	15126.3Mb	39227450	38X	99%	63.8%	0.28%	0.0M	810.5M	100.0%	98.6%	4.5%	810.6M	263.1bp
40PercentNA24385_S10_L001																							23.9%	97.6%	13507.3Mb	101.1M	49.5%	99.2%	19.5%	150.0bp	150.0bp
40PercentNA24385_S10_L002																							24.5%	97.7%	13573.7Mb	101.5M	49.6%	99.2%	19.3%	150.0bp	150.0bp
40PercentNA24385_S10_L003																							23.8%	97.6%	13457.7Mb	100.8M	49.6%	99.2%	19.6%	150.0bp	150.0bp
40PercentNA24385_S10_L004																							23.4%	97.5%	13341.4Mb	100.0M	49.6%	99.2%	19.7%	150.0bp	150.0bp
40PercentNA24385_S10_L005																							24.8%	97.6%	13518.3Mb	101.1M	49.6%	99.2%	19.1%	150.0bp	150.0bp
40PercentNA24385_S10_L006																							23.9%	97.5%	13468.9Mb	100.9M	49.6%	99.2%	19.6%	150.0bp	150.0bp
40PercentNA24385_S10_L007																							25.3%	97.6%	13681.6Mb	102.3M	49.6%	99.2%	19.1%	150.0bp	150.0bp
40PercentNA24385_S10_L008																							26.0%	97.7%	13801.0Mb	103.0M	49.5%	99.2%	18.8%	150.0bp	150.0bp
3140_NA24143	100.0%	100.0%	100.0%	100.0%	100.0%	1238X	1344.6X	0.0X	133886.0X	52744.8Mb	39227450	37X	99%	68.3%	0.29%	0.0M	3363.1M	100.0%	98.4%	4.5%	3363.2M	280.0bp
3140_NA24143_S16_L001																							25.8%	97.5%	56104.2Mb	419.0M	49.6%	99.2%	17.9%	150.0bp	150.0bp
3140_NA24143_S16_L002																							26.3%	97.5%	56355.5Mb	420.5M	49.7%	99.2%	17.7%	150.0bp	150.0bp
3140_NA24143_S16_L003																							25.8%	97.4%	56327.2Mb	421.0M	49.7%	99.2%	17.9%	150.0bp	150.0bp
3140_NA24143_S16_L004																							25.3%	97.4%	55712.9Mb	416.8M	49.7%	99.2%	18.0%	150.0bp	150.0bp
3140_NA24143_S16_L005																							26.6%	97.4%	56591.9Mb	422.4M	49.7%	99.2%	17.5%	150.0bp	150.0bp
3140_NA24143_S16_L006																							25.7%	97.4%	56088.7Mb	419.4M	49.7%	99.2%	17.9%	150.0bp	150.0bp
3140_NA24143_S16_L007																							26.9%	97.5%	56341.3Mb	420.4M	49.7%	99.2%	17.5%	150.0bp	150.0bp
3140_NA24143_S16_L008																							27.6%	97.6%	56869.2Mb	423.6M	49.6%	99.2%	17.2%	150.0bp	150.0bp
3140_NA24385	100.0%	100.0%	100.0%	100.0%	100.0%	1438X	1574.0X	0.0X	155620.0X	61743.5Mb	39227450	35X	99%	76.4%	0.30%	0.0M	5352.2M	100.0%	97.8%	4.8%	5352.4M	340.1bp
3140_NA24385_S9_L001																							32.9%	97.0%	90030.4Mb	666.5M	49.2%	99.0%	12.6%	150.0bp	150.0bp
3140_NA24385_S9_L002																							33.2%	97.0%	90446.5Mb	669.3M	49.3%	99.0%	12.4%	150.0bp	150.0bp
3140_NA24385_S9_L003																							32.5%	96.9%	89451.8Mb	663.0M	49.3%	99.0%	12.7%	150.0bp	150.0bp
3140_NA24385_S9_L004																							32.0%	96.8%	88511.9Mb	656.8M	49.3%	99.0%	12.7%	150.0bp	150.0bp
3140_NA24385_S9_L005																							33.4%	96.8%	90431.4Mb	669.8M	49.3%	99.0%	12.3%	150.0bp	150.0bp
3140_NA24385_S9_L006																							32.5%	96.8%	89544.8Mb	664.0M	49.3%	99.0%	12.7%	150.0bp	150.0bp
3140_NA24385_S9_L007																							33.8%	96.9%	91274.8Mb	675.5M	49.3%	99.0%	12.3%	150.0bp	150.0bp
3140_NA24385_S9_L008																							34.8%	97.0%	93066.1Mb	687.4M	49.2%	99.1%	12.1%	150.0bp	150.0bp
13432478-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
13432478-cfDNA_S21_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13432478-cfDNA_S21_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13432478-cfDNA_S21_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13432478-cfDNA_S21_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13432478-cfDNA_S21_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13432478-cfDNA_S21_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13432478-cfDNA_S21_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13432478-cfDNA_S21_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13511611-cfDNA	100.0%	100.0%	100.0%	100.0%	100.0%	941X	1039.6X	0.0X	88505.0X	40781.5Mb	39227450	41X	99%	69.0%	0.29%	0.0M	2779.3M	100.0%	98.3%	4.6%	2779.4M	219.3bp
13511611-cfDNA_S22_L001																							23.1%	97.6%	47504.7Mb	346.8M	48.4%	99.4%	16.3%	150.0bp	150.0bp
13511611-cfDNA_S22_L002																							23.5%	97.6%	47631.5Mb	347.5M	48.5%	99.4%	16.2%	150.0bp	150.0bp
13511611-cfDNA_S22_L003																							23.1%	97.5%	47572.7Mb	347.5M	48.5%	99.3%	16.3%	150.0bp	150.0bp
13511611-cfDNA_S22_L004																							22.9%	97.5%	47297.3Mb	345.6M	48.5%	99.3%	16.3%	150.0bp	150.0bp
13511611-cfDNA_S22_L005																							23.6%	97.6%	47338.5Mb	345.5M	48.6%	99.4%	16.1%	150.0bp	150.0bp
13511611-cfDNA_S22_L006																							23.2%	97.5%	47680.2Mb	348.4M	48.5%	99.3%	16.3%	150.0bp	150.0bp
13511611-cfDNA_S22_L007																							24.1%	97.6%	47864.4Mb	349.2M	48.5%	99.4%	16.1%	150.0bp	150.0bp
13511611-cfDNA_S22_L008																							24.6%	97.7%	47880.6Mb	349.0M	48.5%	99.4%	15.9%	150.0bp	150.0bp
13739430-cfDNA	95.0%	37.0%	6.0%	0.0%	0.0%	4X	4.4X	0.0X	1861.0X	173.2Mb	39227450	41X	0%	53.9%	0.30%	0.0M	7.6M	100.0%	98.1%	4.4%	7.6M	226.8bp
13739430-cfDNA_S23_L001																							17.2%	97.5%	131.0Mb	1.0M	47.9%	99.3%	15.1%	150.0bp	150.0bp
13739430-cfDNA_S23_L002																							17.7%	97.6%	131.6Mb	1.0M	47.9%	99.3%	14.9%	150.0bp	150.0bp
13739430-cfDNA_S23_L003																							17.3%	97.4%	131.0Mb	1.0M	48.0%	99.3%	15.0%	150.0bp	150.0bp
13739430-cfDNA_S23_L004																							16.9%	97.4%	129.7Mb	0.9M	47.9%	99.3%	15.2%	150.0bp	150.0bp
13739430-cfDNA_S23_L005																							17.9%	97.5%	130.6Mb	1.0M	48.0%	99.3%	14.9%	150.0bp	150.0bp
13739430-cfDNA_S23_L006																							17.4%	97.4%	130.6Mb	1.0M	47.9%	99.3%	15.1%	150.0bp	150.0bp
13739430-cfDNA_S23_L007																							18.4%	97.5%	132.2Mb	1.0M	47.9%	99.3%	14.9%	150.0bp	150.0bp
13739430-cfDNA_S23_L008																							18.9%	97.6%	132.1Mb	1.0M	47.9%	99.3%	14.7%	150.0bp	150.0bp
13929215-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
13929215-cfDNA_S24_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0%	0.0%	150.0bp	150.0bp
13929215-cfDNA_S24_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13929215-cfDNA_S24_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13929215-cfDNA_S24_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13929215-cfDNA_S24_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13929215-cfDNA_S24_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13929215-cfDNA_S24_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
13929215-cfDNA_S24_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
14138939-cfDNA_S25_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA_S25_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA_S25_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA_S25_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA_S25_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA_S25_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA_S25_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14138939-cfDNA_S25_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
14389853-cfDNA_S26_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA_S26_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA_S26_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA_S26_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA_S26_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA_S26_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA_S26_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14389853-cfDNA_S26_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
14558439-cfDNA_S27_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA_S27_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA_S27_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA_S27_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA_S27_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA_S27_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA_S27_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14558439-cfDNA_S27_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
14668865-cfDNA_S28_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA_S28_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA_S28_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA_S28_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA_S28_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA_S28_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA_S28_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14668865-cfDNA_S28_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14862332-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
14862332-cfDNA_S29_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14862332-cfDNA_S29_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0%	0.0%	150.0bp	150.0bp
14862332-cfDNA_S29_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14862332-cfDNA_S29_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0%	0.0%	150.0bp	150.0bp
14862332-cfDNA_S29_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0%	0.0%	150.0bp	150.0bp
14862332-cfDNA_S29_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0%	0.0%	150.0bp	150.0bp
14862332-cfDNA_S29_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
14862332-cfDNA_S29_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0%	0.0%	150.0bp	150.0bp
15451964-cfDNA	100.0%	100.0%	100.0%	100.0%	100.0%	845X	916.6X	0.0X	54761.0X	35957.2Mb	39227450	42X	98%	73.2%	0.28%	0.0M	2937.3M	100.0%	87.5%	4.7%	2937.4M	197.8bp
15451964-cfDNA_S30_L001																							23.9%	97.7%	49642.1Mb	366.0M	48.7%	99.3%	21.9%	150.0bp	150.0bp
15451964-cfDNA_S30_L002																							24.2%	97.7%	49944.4Mb	367.9M	48.8%	99.3%	21.8%	150.0bp	150.0bp
15451964-cfDNA_S30_L003																							23.9%	97.6%	49987.7Mb	368.7M	48.8%	99.3%	21.9%	150.0bp	150.0bp
15451964-cfDNA_S30_L004																							23.9%	97.6%	49727.0Mb	366.9M	48.8%	99.3%	22.0%	150.0bp	150.0bp
15451964-cfDNA_S30_L005																							24.2%	97.7%	49524.5Mb	364.8M	48.8%	99.3%	21.7%	150.0bp	150.0bp
15451964-cfDNA_S30_L006																							24.1%	97.6%	50109.4Mb	369.7M	48.8%	99.3%	21.9%	150.0bp	150.0bp
15451964-cfDNA_S30_L007																							24.8%	97.7%	49960.0Mb	368.1M	48.8%	99.3%	21.7%	150.0bp	150.0bp
15451964-cfDNA_S30_L008																							25.1%	97.7%	49650.7Mb	365.4M	48.7%	99.3%	21.5%	150.0bp	150.0bp
15921737-cfDNA	95.0%	39.0%	7.0%	1.0%	0.0%	4X	4.6X	0.0X	2027.0X	180.0Mb	39227450	40X	0%	65.8%	0.31%	0.0M	10.6M	100.0%	98.3%	4.7%	10.6M	233.1bp
15921737-cfDNA_S31_L001																							22.1%	97.6%	182.0Mb	1.3M	47.9%	99.3%	13.4%	150.0bp	150.0bp
15921737-cfDNA_S31_L002																							22.4%	97.6%	181.4Mb	1.3M	48.0%	99.4%	13.4%	150.0bp	150.0bp
15921737-cfDNA_S31_L003																							22.0%	97.5%	181.2Mb	1.3M	48.0%	99.3%	13.5%	150.0bp	150.0bp
15921737-cfDNA_S31_L004																							21.8%	97.5%	180.4Mb	1.3M	48.0%	99.4%	13.5%	150.0bp	150.0bp
15921737-cfDNA_S31_L005																							22.6%	97.5%	181.0Mb	1.3M	48.0%	99.3%	13.3%	150.0bp	150.0bp
15921737-cfDNA_S31_L006																							22.2%	97.5%	182.1Mb	1.3M	48.0%	99.3%	13.5%	150.0bp	150.0bp
15921737-cfDNA_S31_L007																							23.2%	97.6%	183.0Mb	1.3M	48.0%	99.3%	13.2%	150.0bp	150.0bp
15921737-cfDNA_S31_L008																							23.8%	97.6%	185.8Mb	1.4M	48.0%	99.4%	13.0%	150.0bp	150.0bp
16098090-cfDNA	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
16098090-cfDNA_S32_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
16098090-cfDNA_S32_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
16098090-cfDNA_S32_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
16098090-cfDNA_S32_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
16098090-cfDNA_S32_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
16098090-cfDNA_S32_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
16098090-cfDNA_S32_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
16098090-cfDNA_S32_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q	0.0%	0.0%	0.0%	0.0%	0.0%		0.0X	0.0X	0.0X	0.0Mb	0	0X	0%		0.00%	0.0M	0.0M				0.0M	0.0bp
D0000162_22q_S17_L001																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q_S17_L002																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q_S17_L003																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q_S17_L004																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q_S17_L005																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q_S17_L006																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q_S17_L007																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000162_22q_S17_L008																							0.0%	0.0%	0.0Mb	0.0M	0.0%			0.0bp	0.0bp
D0000476_22q	100.0%	100.0%	100.0%	100.0%	100.0%	559X	570.0X	0.0X	42111.0X	22359.8Mb	39227450	42X	99%	83.2%	0.30%	0.0M	3217.4M	100.0%	89.9%	5.1%	3217.5M	202.8bp
D0000476_22q_S20_L001																							30.4%	97.6%	54692.7Mb	401.7M	47.8%	99.0%	18.8%	150.0bp	150.0bp
D0000476_22q_S20_L002																							30.4%	97.6%	54911.5Mb	403.0M	47.8%	99.0%	18.7%	150.0bp	150.0bp
D0000476_22q_S20_L003																							30.0%	97.5%	54832.5Mb	402.9M	47.9%	99.0%	18.8%	150.0bp	150.0bp
D0000476_22q_S20_L004																							30.3%	97.5%	54651.3Mb	401.7M	47.8%	99.0%	18.9%	150.0bp	150.0bp
D0000476_22q_S20_L005																							30.3%	97.6%	54500.5Mb	400.1M	47.9%	99.0%	18.6%	150.0bp	150.0bp
D0000476_22q_S20_L006																							30.3%	97.5%	54870.3Mb	403.3M	47.9%	99.0%	18.8%	150.0bp	150.0bp
D0000476_22q_S20_L007																							30.9%	97.6%	54880.9Mb	402.8M	47.8%	99.0%	18.6%	150.0bp	150.0bp
D0000476_22q_S20_L008																							31.4%	97.6%	54817.1Mb	402.0M	47.8%	99.0%	18.5%	150.0bp	150.0bp
D0001109_22q	100.0%	100.0%	100.0%	100.0%	100.0%	700X	713.9X	0.0X	55614.0X	28002.9Mb	39227450	41X	99%	77.8%	0.31%	0.0M	2910.7M	100.0%	97.0%	4.8%	2910.8M	216.8bp
D0001109_22q_S19_L001																							27.0%	97.6%	49470.9Mb	361.2M	48.0%	99.1%	16.0%	150.0bp	150.0bp
D0001109_22q_S19_L002																							27.4%	97.6%	50094.3Mb	365.5M	48.1%	99.1%	15.8%	150.0bp	150.0bp
D0001109_22q_S19_L003																							27.0%	97.5%	49992.3Mb	365.2M	48.1%	99.1%	16.0%	150.0bp	150.0bp
D0001109_22q_S19_L004																							27.0%	97.5%	49883.7Mb	364.6M	48.1%	99.0%	16.0%	150.0bp	150.0bp
D0001109_22q_S19_L005																							27.5%	97.5%	50152.3Mb	366.0M	48.1%	99.1%	15.7%	150.0bp	150.0bp
D0001109_22q_S19_L006																							27.1%	97.5%	49778.9Mb	363.8M	48.1%	99.0%	16.0%	150.0bp	150.0bp
D0001109_22q_S19_L007																							27.9%	97.6%	49908.4Mb	364.2M	48.1%	99.1%	15.7%	150.0bp	150.0bp
D0001109_22q_S19_L008																							28.3%	97.6%	49403.1Mb	360.2M	48.0%	99.1%	15.6%	150.0bp	150.0bp
D0001483_22q	100.0%	100.0%	100.0%	100.0%	100.0%	828X	851.2X	0.0X	62263.0X	33391.1Mb	39227450	41X	99%	81.2%	0.29%	0.0M	4092.8M	100.0%	95.1%	4.8%	4093.0M	210.6bp
D0001483_22q_S18_L001																							29.3%	97.5%	69528.3Mb	510.4M	49.1%	99.2%	18.8%	150.0bp	150.0bp
D0001483_22q_S18_L002																							29.4%	97.5%	69899.7Mb	512.7M	49.2%	99.2%	18.6%	150.0bp	150.0bp
D0001483_22q_S18_L003																							29.1%	97.4%	69838.6Mb	512.9M	49.2%	99.2%	18.8%	150.0bp	150.0bp
D0001483_22q_S18_L004																							29.2%	97.4%	69450.4Mb	510.3M	49.2%	99.1%	18.8%	150.0bp	150.0bp
D0001483_22q_S18_L005																							29.4%	97.5%	69428.6Mb	509.4M	49.3%	99.2%	18.5%	150.0bp	150.0bp
D0001483_22q_S18_L006																							29.3%	97.4%	69889.1Mb	513.5M	49.2%	99.1%	18.8%	150.0bp	150.0bp
D0001483_22q_S18_L007																							30.0%	97.5%	69990.8Mb	513.5M	49.2%	99.2%	18.5%	150.0bp	150.0bp
D0001483_22q_S18_L008																							30.4%	97.6%	69593.2Mb	510.1M	49.2%	99.2%	18.4%	150.0bp	150.0bp
SH032_HG513	100.0%	100.0%	100.0%	100.0%	100.0%	380X	436.6X	0.0X	83201.0X	17124.7Mb	39227450	37X	99%	58.8%	0.30%	0.0M	803.0M	100.0%	98.4%	4.5%	803.0M	287.6bp
SH032_HG513_S8_L001																							22.5%	97.4%	13440.5Mb	100.1M	49.6%	99.2%	16.7%	150.0bp	150.0bp
SH032_HG513_S8_L002																							23.1%	97.4%	13549.7Mb	100.8M	49.7%	99.2%	16.5%	150.0bp	150.0bp
SH032_HG513_S8_L003																							22.4%	97.3%	13408.3Mb	100.0M	49.7%	99.2%	16.8%	150.0bp	150.0bp
SH032_HG513_S8_L004																							21.9%	97.3%	13329.8Mb	99.5M	49.7%	99.2%	16.9%	150.0bp	150.0bp
SH032_HG513_S8_L005																							23.4%	97.3%	13573.1Mb	101.1M	49.7%	99.2%	16.4%	150.0bp	150.0bp
SH032_HG513_S8_L006																							22.4%	97.3%	13338.1Mb	99.5M	49.7%	99.2%	16.8%	150.0bp	150.0bp
SH032_HG513_S8_L007																							23.7%	97.4%	13547.1Mb	100.8M	49.6%	99.2%	16.4%	150.0bp	150.0bp
SH032_HG513_S8_L008																							24.5%	97.5%	13632.6Mb	101.3M	49.6%	99.2%	16.1%	150.0bp	150.0bp
SH032_HG514	100.0%	100.0%	100.0%	100.0%	100.0%	1031X	1091.2X	0.0X	109602.0X	42805.6Mb	39227450	37X	99%	72.2%	0.29%	0.0M	3199.9M	100.0%	98.4%	4.6%	3200.0M	283.8bp
SH032_HG514_S1_L001																							27.5%	97.5%	53638.3Mb	399.9M	49.6%	99.1%	17.5%	150.0bp	150.0bp
SH032_HG514_S1_L002																							27.9%	97.5%	53945.0Mb	401.8M	49.7%	99.1%	17.2%	150.0bp	150.0bp
SH032_HG514_S1_L003																							27.2%	97.4%	53152.9Mb	396.6M	49.7%	99.1%	17.4%	150.0bp	150.0bp
SH032_HG514_S1_L004																							26.8%	97.3%	52843.2Mb	394.6M	49.7%	99.1%	17.5%	150.0bp	150.0bp
SH032_HG514_S1_L005																							28.2%	97.4%	53769.2Mb	400.6M	49.7%	99.1%	17.0%	150.0bp	150.0bp
SH032_HG514_S1_L006																							27.2%	97.3%	52979.1Mb	395.5M	49.7%	99.1%	17.5%	150.0bp	150.0bp
SH032_HG514_S1_L007																							28.6%	97.4%	54210.2Mb	403.8M	49.7%	99.1%	17.0%	150.0bp	150.0bp
SH032_HG514_S1_L008																							29.3%	97.5%	54740.9Mb	407.1M	49.6%	99.1%	16.8%	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
1_25PercentHG514	3.6	0.8	47358034.0	1.3	37.9	0.2	210825.3Mb	80515.5Mb	366565.2Mb	61570.8Mb	55.9%	9.4%	657906.0Mb	4786.7M	87.8%	1178.8M	164432.9Mb	1178.7M	4786.7M	7740.3	1569.3	0.6	39227450.0	0.7%
1_25PercentNA24385	2.8	0.8	47358034.0	1.5	38.1	0.3	71516.1Mb	27446.8Mb	126578.0Mb	27678.5Mb	56.3%	12.3%	225541.0Mb	1644.9M	87.8%	507.2M	70337.1Mb	507.2M	1644.9M	2672.8	705.5	0.6	39227450.0	0.6%
2_5PercentHG514	3.5	0.8	47358034.0	1.3	37.7	0.2	211184.8Mb	80905.3Mb	364530.6Mb	61535.6Mb	55.7%	9.4%	656620.7Mb	4777.6M	87.7%	1182.4M	164826.5Mb	1182.3M	4777.6M	7697.3	1568.5	0.6	39227450.0	0.7%
2_5PercentNA24385	3.3	0.8	47358034.0	1.4	37.7	0.2	153725.1Mb	59335.2Mb	265718.9Mb	58835.3Mb	55.7%	12.3%	478779.1Mb	3476.4M	87.6%	1107.6M	153959.3Mb	1107.5M	3476.4M	5610.9	1499.6	0.6	39227450.0	0.6%
5PercentHG514	3.5	0.8	47358034.0	1.5	37.5	0.3	71278.9Mb	27335.1Mb	121526.0Mb	29484.3Mb	55.4%	13.4%	220139.9Mb	1597.4M	87.6%	542.3M	75339.2Mb	542.2M	1597.4M	2566.1	751.5	0.6	39227450.0	0.7%
5PercentNA24385	3.3	0.8	47358034.0	1.4	37.3	0.2	211034.8Mb	82058.3Mb	357806.7Mb	65167.6Mb	55.1%	10.0%	650899.8Mb	4725.1M	87.4%	1250.6M	174703.0Mb	1250.5M	4725.1M	7555.4	1661.0	0.6	39227450.0	0.6%
10PercentHG514	3.4	0.8	47358034.0	1.8	35.5	0.4	2164.2Mb	849.0Mb	3297.8Mb	839.5Mb	52.4%	13.3%	6311.0Mb	45.3M	86.5%	15.2M	2126.9Mb	15.2M	45.3M	69.6	21.4	0.6	39227450.0	0.9%
10PercentNA24385	3.0	0.8	47358034.0	1.3	38.0	0.2	204621.9Mb	79598.0Mb	360265.1Mb	66240.4Mb	56.1%	10.3%	644485.0Mb	4701.1M	87.6%	1263.4M	175887.8Mb	1263.3M	4701.1M	7607.3	1688.4	0.6	39227450.0	0.6%
20PercentHG514	3.6	0.8	47358034.0	1.4	37.6	0.2	159715.3Mb	61318.1Mb	273478.4Mb	56231.9Mb	55.5%	11.4%	494511.8Mb	3585.0M	87.6%	1070.6M	149175.1Mb	1070.5M	3585.0M	5774.7	1433.3	0.6	39227450.0	0.7%
20PercentNA24385	3.5	0.8	47358034.0	1.4	38.0	0.2	176880.0Mb	68560.2Mb	311844.5Mb	62900.1Mb	56.1%	11.3%	557284.8Mb	4057.7M	87.7%	1189.3M	165346.3Mb	1189.0M	4057.7M	6584.8	1603.2	0.6	39227450.0	0.6%
40PercentHG514	3.8	0.8	47358034.0	1.4	37.7	0.3	107609.8Mb	41351.0Mb	185619.0Mb	36750.9Mb	55.6%	11.0%	334579.8Mb	2434.5M	87.6%	689.6M	95886.7Mb	689.6M	2434.5M	3919.5	936.8	0.6	39227450.0	0.7%
40PercentNA24385	3.0	0.8	47358034.0	1.5	38.1	0.3	35324.0Mb	13529.6Mb	62506.7Mb	16332.0Mb	56.3%	14.7%	111360.3Mb	810.6M	87.9%	293.3M	40580.8Mb	293.2M	810.6M	1319.9	416.3	0.6	39227450.0	0.7%
3140_NA24143	3.5	0.8	47358034.0	1.4	37.3	0.2	150341.4Mb	58532.0Mb	254793.4Mb	56442.8Mb	55.1%	12.2%	463666.8Mb	3363.2M	87.4%	1065.1M	148389.3Mb	1065.0M	3363.2M	5380.1	1438.6	0.6	39227450.0	0.7%
3140_NA24385	3.7	0.8	47358034.0	1.4	34.7	0.4	260841.7Mb	104758.0Mb	382521.2Mb	63442.5Mb	51.3%	8.5%	748120.9Mb	5352.4M	86.0%	1262.8M	179248.3Mb	1262.6M	5352.4M	8077.2	1616.9	0.6	39227450.0	0.5%
13432478-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
13511611-cfDNA	0.1	0.8	47358034.0	1.5	40.9	1.7	108196.8Mb	47640.1Mb	235259.6Mb	44424.8Mb	60.3%	11.4%	391096.5Mb	2779.4M	87.8%	862.7M	122183.9Mb	862.6M	2779.4M	4967.7	1132.4	0.7	39227450.0	0.7%
13739430-cfDNA	0.1	0.8	47358034.0	2.4	40.5	3.9	302.5Mb	132.2Mb	643.6Mb	185.9Mb	59.8%	17.3%	1078.4Mb	7.6M	87.7%	3.5M	500.2Mb	3.5M	7.6M	13.6	4.7	0.7	39227450.0	3.5%
13929215-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
14138939-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
14389853-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
14558439-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
14668865-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
14862332-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
15451964-cfDNA	0.1	0.8	47358034.0	1.4	42.4	1.2	106162.2Mb	47666.1Mb	255069.5Mb	40341.6Mb	62.5%	9.9%	408897.9Mb	2937.4M	88.3%	787.1M	110490.7Mb	787.0M	2937.4M	5386.0	1028.4	0.7	39227450.0	0.9%
15921737-cfDNA	0.1	0.8	47358034.0	2.4	40.0	3.4	428.3Mb	186.4Mb	882.1Mb	187.4Mb	59.1%	12.5%	1496.8Mb	10.6M	87.5%	3.6M	516.6Mb	3.6M	10.6M	18.6	4.8	0.7	39227450.0	3.6%
16098090-cfDNA	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
D0000162_22q	0.0	0.8	47358034.0	0.0	0.0	0.0	0.0Mb	0.0Mb	0.0Mb	0.0Mb	0.0%	0.0%	0.0Mb	0.0M	0.0%	0.0M	0.0Mb	0.0M	0.0M	0.0	0.0	0.0	39227450.0	0.0%
D0000476_22q	0.1	0.8	47358034.0	1.2	41.7	3.9	118048.9Mb	55902.4Mb	275981.3Mb	24309.6Mb	61.4%	5.4%	449932.6Mb	3217.5M	87.6%	542.2M	77259.1Mb	542.1M	3217.5M	5827.6	619.7	0.7	39227450.0	0.7%
D0001109_22q	0.1	0.8	47358034.0	1.3	40.9	2.9	111955.4Mb	50750.4Mb	246733.4Mb	30232.7Mb	60.4%	7.4%	409439.2Mb	2910.8M	87.6%	645.6M	91957.2Mb	645.5M	2910.8M	5210.0	770.7	0.7	39227450.0	0.6%
D0001483_22q	1.0	0.8	47358034.0	1.2	41.4	0.4	154568.2Mb	69609.5Mb	349109.1Mb	36589.1Mb	61.0%	6.4%	573286.8Mb	4093.0M	87.9%	769.6M	109599.8Mb	769.4M	4093.0M	7371.7	932.7	0.7	39227450.0	0.7%
SH032_HG513	3.7	0.8	47358034.0	1.5	36.9	0.3	36483.0Mb	14266.2Mb	60345.8Mb	18298.9Mb	54.5%	16.5%	111095.1Mb	803.0M	87.2%	331.0M	45965.5Mb	331.0M	803.0M	1274.2	466.4	0.6	39227450.0	0.7%
SH032_HG514	3.9	0.8	47358034.0	1.3	37.2	0.2	144500.3Mb	55565.4Mb	241869.3Mb	45623.2Mb	54.9%	10.4%	441935.0Mb	3200.0M	87.4%	890.5M	124537.3Mb	890.5M	3200.0M	5107.2	1162.9	0.6	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
1_25PercentHG514	4786.7M	4786.5M	4715.7M	3607.9M	0.0M	216.6M	658031.8Mb	0.0Mb	494406.4Mb	32.5M	1.3M	2129.6M	229.9M
1_25PercentNA24385	1644.9M	1644.9M	1622.1M	1137.7M	0.0M	73.5M	225582.5Mb	0.0Mb	155488.4Mb	10.4M	0.4M	728.8M	82.8M
2_5PercentHG514	4777.6M	4777.5M	4704.6M	3595.2M	0.0M	216.1M	656746.7Mb	0.0Mb	492699.1Mb	33.5M	1.3M	2126.7M	227.3M
2_5PercentNA24385	3476.4M	3476.3M	3423.2M	2368.8M	0.0M	157.3M	478870.1Mb	0.0Mb	325461.7Mb	24.3M	0.9M	1550.3M	162.6M
5PercentHG514	1597.4M	1597.4M	1574.1M	1055.2M	0.0M	72.0M	220182.9Mb	0.0Mb	145092.1Mb	10.7M	0.4M	713.8M	73.8M
5PercentNA24385	4725.1M	4724.9M	4646.4M	3474.5M	0.0M	214.5M	651023.1Mb	0.0Mb	477115.6Mb	36.1M	1.4M	2108.7M	216.3M
10PercentHG514	45.3M	45.3M	44.5M	30.2M	0.0M	2.1M	6312.2Mb	0.0Mb	4192.5Mb	0.4M	0.0M	20.6M	1.6M
10PercentNA24385	4701.1M	4701.0M	4627.4M	3437.7M	0.0M	213.0M	644605.7Mb	0.0Mb	469463.0Mb	33.7M	1.3M	2080.2M	235.2M
20PercentHG514	3585.0M	3584.8M	3531.9M	2514.3M	0.0M	161.8M	494611.1Mb	0.0Mb	346034.6Mb	24.2M	1.0M	1604.1M	163.1M
20PercentNA24385	4057.7M	4057.3M	3995.1M	2868.4M	0.0M	184.6M	557392.0Mb	0.0Mb	392739.9Mb	28.5M	1.1M	1799.6M	199.5M
40PercentHG514	2434.5M	2434.4M	2393.9M	1744.9M	0.0M	111.3M	334644.1Mb	0.0Mb	239145.9Mb	18.6M	0.7M	1082.3M	115.5M
40PercentNA24385	810.6M	810.5M	799.6M	517.3M	0.0M	36.4M	111381.6Mb	0.0Mb	70921.8Mb	5.0M	0.2M	360.0M	40.0M
3140_NA24143	3363.2M	3363.1M	3309.0M	2298.1M	0.0M	153.0M	463754.5Mb	0.0Mb	315906.7Mb	24.8M	1.0M	1502.1M	153.7M
3140_NA24385	5352.4M	5352.1M	5237.0M	4089.6M	0.0M	255.4M	748261.0Mb	0.0Mb	570032.0Mb	52.9M	2.3M	2451.2M	169.8M
13432478-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
13511611-cfDNA	2779.4M	2779.3M	2732.4M	1916.7M	0.0M	127.5M	391181.6Mb	0.0Mb	269428.1Mb	11.3M	0.6M	1258.7M	119.0M
13739430-cfDNA	7.6M	7.6M	7.5M	4.1M	0.0M	0.3M	1078.6Mb	0.0Mb	579.4Mb	0.0M	0.0M	3.5M	0.3M
13929215-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
14138939-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
14389853-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
14558439-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
14668865-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
14862332-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
15451964-cfDNA	2937.4M	2937.3M	2570.0M	2150.3M	0.0M	139.4M	408989.6Mb	0.0Mb	298967.5Mb	14.8M	3.1M	1280.6M	170.2M
15921737-cfDNA	10.6M	10.6M	10.5M	7.0M	0.0M	0.5M	1497.1Mb	0.0Mb	982.1Mb	0.1M	0.0M	4.9M	0.4M
16098090-cfDNA	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
D0000162_22q	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
D0000476_22q	3217.5M	3217.3M	2891.4M	2675.3M	0.0M	163.0M	450036.3Mb	0.0Mb	373371.2Mb	28.1M	3.1M	1417.8M	159.6M
D0001109_22q	2910.8M	2910.7M	2823.1M	2265.2M	0.0M	139.4M	409535.0Mb	0.0Mb	318124.6Mb	24.9M	1.2M	1307.0M	122.3M
D0001483_22q	4093.0M	4092.8M	3893.8M	3323.4M	0.0M	197.8M	573408.6Mb	0.0Mb	464535.7Mb	29.4M	2.1M	1813.1M	201.8M
SH032_HG513	803.0M	803.0M	789.9M	472.0M	0.0M	36.5M	111118.2Mb	0.0Mb	65273.9Mb	6.0M	0.2M	361.3M	34.0M
SH032_HG514	3200.0M	3199.8M	3147.9M	2309.4M	0.0M	146.0M	442020.4Mb	0.0Mb	318012.2Mb	23.8M	1.0M	1434.3M	140.9M

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`

20260529_LH00995_0049_B23YT2HLT4

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Mosdepth

Cumulative coverage distribution Help

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Average coverage per contig

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Picard

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Hybrid-selection target coverage

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Samtools

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Alignment stats

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Samtools: stats: Alignment Stats: Columns

fastp

Filtered Reads

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