MultiQC Report

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

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Report generated on 2022-12-21, 16:01 based on data in: /data/input/appresults

General Statistics

Showing ¹²/₁₂ rows and ⁸/₂₃ columns.

Sample Name	M Input reads	Paired	QC-fail	Map	Unmap	Dup	Uniq map	Prop pair	Discord	Diff chr, MQ⩾10	Med IS	Q30	M Alignments	Sec'ry	Contam'n	Sex	M Aln reads	Mb Aln bases	Reads on target	Bases on target	Depth	Uniformity (>0.2×mean)	Mean/med autosomal coverage
Sample-01	889.5	100.0%	0.00%	77.7%	22.3%	12.7%	65.0%	72.8%	0.19%	0.03%	187	88.9%	691.1	0.00%	NA	X0	539.2	79625.9	100.0%	100.0%	26.3 x	91.9 %	0.96
Sample-02	1248.5	100.0%	0.00%	82.0%	18.0%	26.8%	55.2%	77.2%	0.21%	0.03%	189	90.2%	1023.8	0.00%	NA	X0	637.9	94227.8	100.0%	100.0%	31.1 x	91.9 %	0.97
Sample-03	968.0	100.0%	0.00%	77.5%	22.5%	13.8%	63.6%	72.7%	0.20%	0.03%	187	89.2%	749.9	0.00%	NA	X0	574.4	84815.4	100.0%	100.0%	28.0 x	92.0 %	0.96
Sample-04	928.4	100.0%	0.00%	75.8%	24.1%	12.4%	63.5%	70.7%	0.19%	0.03%	187	88.0%	704.2	0.00%	NA	X0	548.8	81030.4	100.0%	100.0%	26.7 x	91.9 %	0.95
Sample-05	739.1	100.0%	0.00%	74.7%	25.3%	11.4%	63.3%	69.7%	0.16%	0.03%	186	87.1%	551.9	0.00%	NA	X0	435.5	64308.2	100.0%	100.0%	21.2 x	91.6 %	0.98
Sample-06	871.0	100.0%	0.00%	76.0%	24.1%	13.6%	62.4%	71.0%	0.19%	0.03%	187	88.8%	661.6	0.00%	NA	X0	505.8	74676.0	100.0%	100.0%	24.6 x	92.1 %	0.97
Sample-07	1165.4	100.0%	0.00%	76.0%	24.0%	14.8%	61.2%	70.5%	0.20%	0.03%	185	88.3%	885.4	0.00%	NA	X0	664.2	98033.1	100.0%	100.0%	32.3 x	92.0 %	0.96
Sample-08	1184.0	100.0%	0.00%	78.5%	21.5%	17.2%	61.3%	71.9%	0.20%	0.04%	186	86.2%	929.5	0.00%	NA	X0	674.2	99612.5	100.0%	100.0%	32.8 x	92.0 %	0.97
Sample-09	851.0	100.0%	0.00%	77.3%	22.7%	13.7%	63.6%	71.3%	0.25%	0.03%	188	87.9%	657.8	0.00%	NA	X0	503.8	74449.2	100.0%	100.0%	24.6 x	92.1 %	0.97
Sample-10	881.9	100.0%	0.00%	80.0%	19.9%	18.6%	61.4%	74.0%	0.31%	0.04%	188	87.7%	706.0	0.00%	NA	X0	502.3	74150.7	100.0%	100.0%	24.4 x	92.0 %	0.96
Sample-11	819.7	100.0%	0.00%	79.1%	20.9%	17.2%	61.9%	73.2%	0.50%	0.04%	192	88.9%	648.3	0.00%	NA	X0	472.8	69910.6	100.0%	100.0%	23.1 x	92.1 %	0.98
Sample-12	799.8	100.0%	0.00%	78.7%	21.4%	16.7%	62.0%	72.6%	0.52%	0.04%	193	88.7%	629.0	0.00%	NA	X0	461.8	68287.6	100.0%	100.0%	22.5 x	92.0 %	0.96

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Sort	Group	Column	Description	ID	Scale
\|\|	DRAGEN mapping	M Input reads	Total number of input reads for this sample (or total number of reads in all input read groups combined), millions	`Total input reads`	read_count
\|\|	DRAGEN mapping	Paired	% of reads with a mate sequenced	`Reads with mate sequenced pct`	None
\|\|	DRAGEN mapping	QC-fail	% of reads not passing platform/vendor quality checks (SAM flag 0x200)	`QC-failed reads pct`	None
\|\|	DRAGEN mapping	Map	% of mapped reads	`Mapped reads pct`	None
\|\|	DRAGEN mapping	Unmap	% of unmapped reads	`Unmapped reads pct`	None
\|\|	DRAGEN mapping	Dup	% of duplicate marked reads as a result of the --enable-duplicatemarking option being used	`Number of duplicate marked reads pct`	None
\|\|	DRAGEN mapping	Uniq map	% of unique & mapped reads (mapped reads minus duplicate marked reads)	`Number of unique & mapped reads (excl. duplicate marked reads) pct`	None
\|\|	DRAGEN mapping	Prop pair	% of properly paired reads (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`Properly paired reads pct`	None
\|\|	DRAGEN mapping	Discord	% of discordant reads: paired reads minus properly paired reads	`Not properly paired reads (discordant) pct`	None
\|\|	DRAGEN mapping	Diff chr, MQ⩾10	% of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome	`Paired reads mapped to different chromosomes (MAPQ>=10) pct`	None
\|\|	DRAGEN mapping	Med IS	Median insert size	`Insert length: median`	None
\|\|	DRAGEN mapping	Q30	% of raw bases with BQ >= 30	`Q30 bases pct`	None
\|\|	DRAGEN mapping	M Alignments	Total number of alignments with MQ > 0, millions	`Total alignments`	read_count
\|\|	DRAGEN mapping	Sec'ry	% of secondary alignments. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`Secondary alignments pct`	None
\|\|	DRAGEN mapping	Contam'n	Fraction of estimated sample contamination	`Estimated sample contamination`	None
\|\|	Ploidy estimation	Sex	Sex chromosome ploidy estimation (XX, XY, X0, 00, etc.)	`Ploidy estimation`	None
\|\|	DRAGEN coverage	M Aln reads	Total number of aligned reads.	`Aligned reads`	read_count
\|\|	DRAGEN coverage	Mb Aln bases	Total number of aligned bases.	`Aligned bases`	base_count
\|\|	DRAGEN coverage	Reads on target	% of uniquely mapped reads to region relative to the number of uniquely mapped reads to the genome. When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region.	`Aligned reads in genome pct`	None
\|\|	DRAGEN coverage	Bases on target	% of uniquely mapped bases to the region relative to the number of uniquely mapped bases to the genome.	`Aligned bases in genome pct`	None
\|\|	DRAGEN coverage	Depth	Coverage depth over genome: number of uniquely mapped bases to genome divided by the number of sites in genome.	`Average alignment coverage over genome`	None
\|\|	DRAGEN coverage	Uniformity (>0.2×mean)	Percentage of sites with coverage greater than 20% of the mean coverage in region. Demonstrates the uniformity of coverage. The lower the better.	`Uniformity of coverage (PCT > 0.2*mean) over genome`	None
\|\|	DRAGEN coverage	Mean/med autosomal coverage	Mean autosomal coverage in genome divided by the median autosomal coverage in genome. If there is no autosome in the reference genome or the region does not intersect autosomes, this metric shows as NA.	`Mean/Median autosomal coverage ratio over genome`	None

DRAGEN

DRAGEN is a Bio-IT Platform that provides ultra-rapid secondary analysis of sequencing data using field-programmable gate array technology (FPGA).

Mapping metrics

Mapping metrics, similar to the metrics computed by the samtools-stats command. Shown on per read group level. To see per-sample level metrics, refer to the general stats table.

Showing ¹⁵/₁₅ rows and ¹²/₇₀ columns.

Sample Name	Input reads	M Input reads	Paired	M Paired	Single	QC-fail	Map	M Map	Map R1	M Map R1	Map R2	M Map R2	Unmap	M Unmap	MQ⩾40	M MQ⩾40	Dup	Uniq	Uniq map	M Uniq map	Self & mate map	M Self & mate map	Prop pair	M Prop pair	Discord	M Discord	Singleton	M Singleton	Diff chrom	M Diff chrom	Diff chr, MQ⩾10	M Diff chr, MQ⩾10	Reads with indel R1	M Reads with indel R1	Reads with indel R2	M Reads with indel R2	Read len	Avg IS	Med IS	IS std	Mb Input bases	Mb Input bases R1	Mb Input bases R2	Mapped bases R1	Mb Mapped bases R1	Mapped bases R2	Mb Mapped bases R2	Soft-clip bases R1	Soft-clip bases R2	MM bases R1	Mb MM bases R1	MM bases R2	MM bases R1 excl indels	Mb MM bases R1 excl indels	MM bases R2 excl indels	Q30	Mb Q30	Q30 R1	Mb Q30 R1	Q30 R2	Mb Q30 R2	Q30 excl dup & clipped	Mb Q30 excl dup & clipped	M Alignments	Sec'ry
Sample-01_L2	100.0%	889.5	100.0%	889.5	0.0%	0.00%	77.7%	691.1	79.5%	353.6	75.9%	337.5	22.3%	198.4	67.8%	602.8	12.7%	87.3%	65.0%	578.5	73.0%	649.2	72.8%	647.6	0.19%	1.68	4.71%	41.89	0.09%	0.55	0.03%	0.19	20.8%	73.6	67.8%	229.0	151.0	195.1	187	42.4	134320.2	67160.1	67160.1	39.7%	53390.9	37.9%	50968.3	0.0%	0.0%	21.0%	11188.8	23.9%	19.8%	10547.9	20.4%	88.9%	119351.4	88.4%	59383.7	89.3%	59967.7	77.6%	104233.8	691.1	0.00%
Sample-02_L4	100.0%	1248.5	100.0%	1248.5	0.0%	0.00%	82.0%	1023.8	83.9%	523.9	80.1%	499.9	18.0%	224.7	71.8%	897.0	26.8%	73.2%	55.2%	689.2	77.4%	966.3	77.2%	963.6	0.21%	2.68	4.60%	57.46	0.10%	0.92	0.03%	0.32	20.7%	108.2	67.6%	337.8	151.0	196.1	189	42.6	188522.0	94261.0	94261.0	42.0%	79110.6	40.0%	75481.1	0.0%	0.0%	20.9%	16528.4	23.9%	19.8%	15624.2	20.4%	90.2%	170140.7	90.3%	85087.6	90.2%	85053.1	66.1%	124573.6	1023.8	0.00%
Sample-03_L3	100.0%	968.0	100.0%	968.0	0.0%	0.00%	77.5%	749.9	79.6%	385.4	75.3%	364.5	22.5%	218.1	67.7%	654.8	13.8%	86.2%	63.6%	616.1	72.9%	705.6	72.7%	703.7	0.20%	1.95	4.57%	44.25	0.09%	0.61	0.03%	0.21	21.3%	82.2	67.4%	245.8	151.0	194.5	187	42.1	146169.7	73084.8	73084.8	39.8%	58188.9	37.7%	55042.8	0.0%	0.0%	21.0%	12214.0	23.9%	19.8%	11489.5	20.4%	89.2%	130391.2	89.3%	65235.0	89.2%	65156.3	76.9%	112371.2	749.9	0.00%
Sample-04_L1	100.0%	284.1	100.0%	284.1	0.0%	0.00%	76.2%	216.3	78.5%	111.6	73.8%	104.8	23.8%	67.7	66.2%	188.0	17.8%	82.2%	58.3%	165.7	71.1%	201.8	70.9%	201.3	0.18%	0.52	5.10%	14.49	0.08%	0.16	0.03%	0.05	21.3%	23.7	67.4%	70.6	151.0	195.2	188	42.1	42892.5	21446.3	21446.3	39.3%	16844.9	36.9%	15821.4	0.0%	0.0%	21.0%	3543.5	23.9%	19.8%	3335.6	20.5%	87.4%	37495.2	87.7%	18799.2	87.2%	18696.0	71.8%	30793.0	216.3	0.00%
Sample-04_L4	100.0%	644.3	100.0%	644.3	0.0%	0.00%	75.7%	487.9	77.7%	250.5	73.7%	237.4	24.3%	156.5	65.8%	424.1	10.0%	90.0%	65.7%	423.6	70.8%	456.4	70.6%	455.1	0.19%	1.23	4.89%	31.51	0.09%	0.40	0.03%	0.14	21.6%	54.1	67.5%	160.2	151.0	193.9	187	42.0	97296.0	48648.0	48648.0	38.9%	37819.7	36.8%	35848.2	0.0%	0.0%	21.1%	7963.7	23.9%	19.8%	7483.4	20.5%	88.2%	85839.4	87.9%	42749.0	88.6%	43090.3	79.4%	77281.2	487.9	0.00%
Sample-05_L1	100.0%	520.5	100.0%	520.5	0.0%	0.00%	74.2%	386.2	76.2%	198.4	72.2%	187.9	25.8%	134.2	64.5%	335.5	12.0%	88.0%	62.2%	323.7	69.4%	361.3	69.3%	360.5	0.16%	0.82	4.80%	24.96	0.08%	0.28	0.03%	0.09	21.7%	43.0	67.3%	126.5	151.0	194.4	187	42.0	78589.2	39294.6	39294.6	38.1%	29955.4	36.1%	28366.3	0.0%	0.0%	21.0%	6297.2	23.9%	19.8%	5915.5	20.4%	86.9%	68315.9	86.4%	33940.2	87.5%	34375.7	76.5%	60113.9	386.2	0.00%
Sample-05_L4	100.0%	218.7	100.0%	218.7	0.0%	0.00%	75.8%	165.7	77.7%	84.9	73.8%	80.7	24.2%	53.0	65.9%	144.1	9.9%	90.1%	65.9%	144.1	71.0%	155.2	70.8%	154.8	0.18%	0.39	4.80%	10.50	0.08%	0.13	0.03%	0.04	21.5%	18.2	67.2%	54.2	151.0	192.2	185	40.7	33018.2	16509.1	16509.1	38.8%	12823.8	36.9%	12192.1	0.0%	0.0%	21.1%	2702.4	23.9%	19.8%	2540.9	20.4%	87.5%	28906.8	86.9%	14350.7	88.2%	14556.1	78.9%	26064.0	165.7	0.00%
Sample-06_L1	100.0%	871.0	100.0%	871.0	0.0%	0.00%	76.0%	661.6	78.2%	340.4	73.8%	321.2	24.1%	209.5	66.1%	575.8	13.6%	86.4%	62.4%	543.3	71.2%	619.9	71.0%	618.3	0.19%	1.66	4.78%	41.63	0.09%	0.55	0.03%	0.19	21.6%	73.7	67.5%	216.9	151.0	194.0	187	41.9	131526.5	65763.3	65763.3	39.1%	51398.9	36.9%	48498.3	0.0%	0.0%	21.0%	10794.0	23.9%	19.7%	10139.2	20.4%	88.8%	116846.9	88.8%	58400.7	88.9%	58446.2	76.8%	100960.6	661.6	0.00%
Sample-07_L2	100.0%	1165.4	100.0%	1165.4	0.0%	0.00%	76.0%	885.4	78.3%	456.4	73.6%	429.0	24.0%	280.0	65.9%	768.3	14.8%	85.2%	61.2%	713.6	70.7%	823.4	70.5%	821.1	0.20%	2.34	5.32%	61.99	0.07%	0.61	0.03%	0.21	22.0%	100.5	67.9%	291.1	151.0	191.1	185	38.7	175980.1	87990.0	87990.0	39.2%	68919.4	36.8%	64781.7	0.0%	0.0%	20.1%	13885.2	23.1%	18.9%	12991.2	19.6%	88.3%	155483.1	88.3%	77741.7	88.3%	77741.4	75.3%	132508.8	885.4	0.00%
Sample-08_L2	100.0%	1184.0	100.0%	1184.0	0.0%	0.00%	78.5%	929.5	82.6%	488.9	74.4%	440.6	21.5%	254.5	68.2%	807.4	17.2%	82.8%	61.3%	725.6	72.1%	854.0	71.9%	851.6	0.20%	2.41	6.37%	75.44	0.10%	0.88	0.04%	0.31	20.8%	101.4	67.5%	297.2	151.0	192.2	186	39.1	178789.1	89394.6	89394.6	41.3%	73828.7	37.2%	66523.6	0.0%	0.0%	20.1%	14815.0	23.2%	18.9%	13938.3	19.7%	86.2%	154202.0	86.9%	77661.6	85.6%	76540.5	71.3%	127558.8	929.5	0.00%
Sample-09_L1	100.0%	191.8	100.0%	191.8	0.0%	0.00%	77.5%	148.6	79.3%	76.0	75.7%	72.6	22.5%	43.2	67.4%	129.3	19.2%	80.8%	58.3%	111.9	72.0%	138.2	71.8%	137.8	0.24%	0.46	5.42%	10.39	0.09%	0.13	0.03%	0.04	20.6%	15.7	67.2%	48.8	151.0	194.9	189	40.3	28967.4	14483.7	14483.7	39.6%	11482.2	37.8%	10958.5	0.0%	0.0%	20.1%	2309.8	23.1%	18.9%	2176.4	19.6%	87.7%	25410.3	87.4%	12663.0	88.0%	12747.4	70.8%	20522.8	148.6	0.00%
Sample-09_L3	100.0%	659.2	100.0%	659.2	0.0%	0.00%	77.2%	509.2	79.2%	261.2	75.2%	248.0	22.8%	150.1	67.0%	441.5	12.1%	87.9%	65.2%	429.6	71.5%	471.1	71.2%	469.5	0.25%	1.65	5.77%	38.06	0.10%	0.46	0.03%	0.15	20.2%	52.8	67.0%	166.2	151.0	193.7	188	38.6	99540.9	49770.4	49770.4	39.6%	39436.8	37.6%	37446.4	0.0%	0.0%	20.1%	7933.0	23.1%	19.0%	7485.0	19.7%	88.0%	87590.2	87.6%	43584.0	88.4%	44006.2	77.3%	76980.4	509.2	0.00%
Sample-10_L3	100.0%	881.9	100.0%	881.9	0.0%	0.00%	80.0%	706.0	81.8%	360.6	78.3%	345.5	19.9%	175.9	69.5%	613.0	18.6%	81.4%	61.4%	541.9	74.3%	655.1	74.0%	652.4	0.31%	2.69	5.77%	50.88	0.11%	0.71	0.04%	0.25	19.7%	71.1	69.1%	238.8	151.0	193.1	188	38.5	133169.4	66584.7	66584.7	40.9%	54444.8	39.2%	52163.0	0.0%	0.0%	19.7%	10725.5	22.9%	18.6%	10133.1	19.3%	87.7%	116773.1	87.2%	58090.6	88.1%	58682.5	71.3%	95014.4	706.0	0.00%
Sample-11_L4	100.0%	819.7	100.0%	819.7	0.0%	0.00%	79.1%	648.3	82.2%	336.8	76.0%	311.5	20.9%	171.4	69.2%	567.4	17.2%	82.8%	61.9%	507.1	73.7%	604.1	73.2%	600.1	0.50%	4.08	5.39%	44.20	0.13%	0.79	0.04%	0.24	19.3%	64.9	66.6%	207.4	151.0	200.7	192	46.6	123779.7	61889.9	61889.9	41.1%	50857.6	38.0%	47042.6	0.0%	0.0%	21.2%	10783.5	24.2%	20.2%	10253.9	20.8%	88.9%	110041.4	89.5%	55392.4	88.3%	54649.0	73.6%	91056.6	648.3	0.00%
Sample-12_L4	100.0%	799.8	100.0%	799.8	0.0%	0.00%	78.7%	629.0	81.9%	327.5	75.4%	301.6	21.4%	170.8	68.7%	549.5	16.7%	83.3%	62.0%	495.5	73.1%	584.5	72.6%	580.3	0.52%	4.18	5.57%	44.52	0.14%	0.81	0.04%	0.24	19.5%	63.8	66.4%	200.4	151.0	201.1	193	47.3	120775.6	60387.8	60387.8	40.9%	49451.4	37.7%	45534.6	0.0%	0.0%	21.2%	10505.7	24.2%	20.2%	9980.3	20.8%	88.7%	107166.7	89.4%	54002.9	88.0%	53163.8	73.9%	89244.0	629.0	0.00%

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

Sort	Group	Column	Description	ID	Scale
\|\|	DRAGEN mapping	Input reads	Total number of reads in this RG	`Total reads in RG pct`	None
\|\|	DRAGEN mapping	M Input reads	Total number of reads in this RG, millions	`Total reads in RG`	read_count
\|\|	DRAGEN mapping	Paired	% of reads with a mate sequenced	`Reads with mate sequenced pct`	None
\|\|	DRAGEN mapping	M Paired	Number of reads with a mate sequenced, millions	`Reads with mate sequenced`	read_count
\|\|	DRAGEN mapping	Single	% of reads without a mate sequenced	`Reads without mate sequenced pct`	None
\|\|	DRAGEN mapping	M Single	Number of reads without a mate sequenced, millions	`Reads without mate sequenced`	read_count
\|\|	DRAGEN mapping	QC-fail	% of reads not passing platform/vendor quality checks (SAM flag 0x200)	`QC-failed reads pct`	None
\|\|	DRAGEN mapping	M QC-fail	Number of reads not passing platform/vendor quality checks (SAM flag 0x200), millions	`QC-failed reads`	read_count
\|\|	DRAGEN mapping	Map	% of mapped reads	`Mapped reads pct`	None
\|\|	DRAGEN mapping	M Map	Number of mapped reads, millions	`Mapped reads`	read_count
\|\|	DRAGEN mapping	Map R1	% of mapped reads R1	`Mapped reads R1 pct`	None
\|\|	DRAGEN mapping	M Map R1	Number of mapped reads R1, millions	`Mapped reads R1`	read_count
\|\|	DRAGEN mapping	Map R2	% of mapped reads R2	`Mapped reads R2 pct`	None
\|\|	DRAGEN mapping	M Map R2	Number of mapped reads R2, millions	`Mapped reads R2`	read_count
\|\|	DRAGEN mapping	Unmap	% of unmapped reads	`Unmapped reads pct`	None
\|\|	DRAGEN mapping	M Unmap	Number of unmapped reads, millions	`Unmapped reads`	read_count
\|\|	DRAGEN mapping	MQ⩾40	% of reads with MAPQ [40:inf)	`Reads with MAPQ [40:inf) pct`	None
\|\|	DRAGEN mapping	M MQ⩾40	Number of reads with MAPQ [40:inf), millions	`Reads with MAPQ [40:inf)`	read_count
\|\|	DRAGEN mapping	Dup	% of duplicate marked reads as a result of the --enable-duplicatemarking option being used	`Number of duplicate marked reads pct`	None
\|\|	DRAGEN mapping	Uniq	% of unique reads (all reads minus duplicate marked reads)	`Number of unique reads (excl. duplicate marked reads) pct`	None
\|\|	DRAGEN mapping	Uniq map	% of unique & mapped reads (mapped reads minus duplicate marked reads)	`Number of unique & mapped reads (excl. duplicate marked reads) pct`	None
\|\|	DRAGEN mapping	M Uniq map	Number of unique & mapped reads (mapped reads minus duplicate marked reads), millions	`Number of unique & mapped reads (excl. duplicate marked reads)`	read_count
\|\|	DRAGEN mapping	Self & mate map	% of reads mapped in pairs (itself & mate mapped)	`Paired reads (itself & mate mapped) pct`	None
\|\|	DRAGEN mapping	M Self & mate map	Number of reads mapped in pairs (itself & mate mapped), millions	`Paired reads (itself & mate mapped)`	read_count
\|\|	DRAGEN mapping	Prop pair	% of properly paired reads (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`Properly paired reads pct`	None
\|\|	DRAGEN mapping	M Prop pair	Number of properly paired reads, millions (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`Properly paired reads`	read_count
\|\|	DRAGEN mapping	Discord	% of discordant reads: paired reads minus properly paired reads	`Not properly paired reads (discordant) pct`	None
\|\|	DRAGEN mapping	M Discord	Number of discordant reads: paired reads minus properly paired reads , millions	`Not properly paired reads (discordant)`	read_count
\|\|	DRAGEN mapping	Singleton	% of singleton reads: itself mapped; mate unmapped	`Singleton reads (itself mapped; mate unmapped) pct`	None
\|\|	DRAGEN mapping	M Singleton	Number of singleton reads: itself mapped; mate unmapped, millions	`Singleton reads (itself mapped; mate unmapped)`	read_count
\|\|	DRAGEN mapping	Diff chrom	% of paired reads with a mate mapped to a different chromosome	`Paired reads mapped to different chromosomes pct`	None
\|\|	DRAGEN mapping	M Diff chrom	Number of paired reads with a mate mapped to a different chromosome, millions	`Paired reads mapped to different chromosomes`	read_count
\|\|	DRAGEN mapping	Diff chr, MQ⩾10	% of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome	`Paired reads mapped to different chromosomes (MAPQ>=10) pct`	None
\|\|	DRAGEN mapping	M Diff chr, MQ⩾10	Number of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome, millions	`Paired reads mapped to different chromosomes (MAPQ>=10)`	read_count
\|\|	DRAGEN mapping	Reads with indel R1	% of R1 reads containing at least 1 indel	`Reads with indel R1 pct`	None
\|\|	DRAGEN mapping	M Reads with indel R1	Number of R1 reads containing at least 1 indel, millions	`Reads with indel R1`	read_count
\|\|	DRAGEN mapping	Reads with indel R2	% of R2 reads containing at least 1 indel	`Reads with indel R2 pct`	None
\|\|	DRAGEN mapping	M Reads with indel R2	Number of R2 reads containing at least 1 indel, millions	`Reads with indel R2`	read_count
\|\|	DRAGEN mapping	Read len	Estimated read length. Total number of input bases divided by the number of reads	`Estimated read length`	None
\|\|	DRAGEN mapping	Avg IS	Mean insert size	`Insert length: mean`	None
\|\|	DRAGEN mapping	Med IS	Median insert size	`Insert length: median`	None
\|\|	DRAGEN mapping	IS std	Standard deviation of insert size deviation	`Insert length: standard deviation`	None
\|\|	DRAGEN mapping	Mb Input bases	Total number of bases sequenced, millions	`Total bases`	base_count
\|\|	DRAGEN mapping	Mb Input bases R1	Total number of bases sequenced on R1 reads, millions	`Total bases R1`	base_count
\|\|	DRAGEN mapping	Mb Input bases R2	Total number of bases sequenced on R2 reads, millions	`Total bases R2`	base_count
\|\|	DRAGEN mapping	Mapped bases R1	% of mapped bases on R1 reads	`Mapped bases R1 pct`	None
\|\|	DRAGEN mapping	Mb Mapped bases R1	Number of mapped bases on R1 reads, millions	`Mapped bases R1`	base_count
\|\|	DRAGEN mapping	Mapped bases R2	% of mapped bases on R2 reads	`Mapped bases R2 pct`	None
\|\|	DRAGEN mapping	Mb Mapped bases R2	Number of mapped bases on R2 reads, millions	`Mapped bases R2`	base_count
\|\|	DRAGEN mapping	Soft-clip bases R1	% of soft-clipped bases on R1 reads	`Soft-clipped bases R1 pct`	None
\|\|	DRAGEN mapping	Mb Soft-clip bases R1	Number of soft-clipped bases on R1 reads, millions	`Soft-clipped bases R1`	base_count
\|\|	DRAGEN mapping	Soft-clip bases R2	% of soft-clipped bases on R2 reads	`Soft-clipped bases R2 pct`	None
\|\|	DRAGEN mapping	MM bases R1	% of mismatched bases on R1, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1 pct`	None
\|\|	DRAGEN mapping	Mb MM bases R1	Number of mismatched bases on R1, millions, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1`	base_count
\|\|	DRAGEN mapping	MM bases R2	% of mismatched bases on R2, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R2 pct`	None
\|\|	DRAGEN mapping	MM bases R1 excl indels	% of mismatched bases on R1. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1 (excl. indels) pct`	None
\|\|	DRAGEN mapping	Mb MM bases R1 excl indels	Number of mismatched bases on R1, millions. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1 (excl. indels)`	base_count
\|\|	DRAGEN mapping	MM bases R2 excl indels	% of mismatched bases on R2. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R2 (excl. indels) pct`	None
\|\|	DRAGEN mapping	Q30	% of raw bases with BQ >= 30	`Q30 bases pct`	None
\|\|	DRAGEN mapping	Mb Q30	Number of raw bases with BQ >= 30, millions	`Q30 bases`	base_count
\|\|	DRAGEN mapping	Q30 R1	% of raw bases on R1 reads with BQ >= 30	`Q30 bases R1 pct`	None
\|\|	DRAGEN mapping	Mb Q30 R1	Number of raw bases on R1 reads with BQ >= 30, millions	`Q30 bases R1`	base_count
\|\|	DRAGEN mapping	Q30 R2	% of raw bases on R2 reads with BQ >= 30	`Q30 bases R2 pct`	None
\|\|	DRAGEN mapping	Mb Q30 R2	Number of raw bases on R2 reads with BQ >= 30, millions	`Q30 bases R2`	base_count
\|\|	DRAGEN mapping	Q30 excl dup & clipped	% of non-clipped bases with BQ >= 30 on non-duplicate reads	`Q30 bases (excl. dups & clipped bases) pct`	None
\|\|	DRAGEN mapping	Mb Q30 excl dup & clipped	Number of non-clipped bases with BQ >= 30 on non-duplicate reads, millions	`Q30 bases (excl. dups & clipped bases)`	base_count
\|\|	DRAGEN mapping	M Alignments	Total number of alignments with MQ > 0, millions	`Total alignments`	read_count
\|\|	DRAGEN mapping	Sec'ry	% of secondary alignments. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`Secondary alignments pct`	None
\|\|	DRAGEN mapping	M Sec'ry	Number of secondary alignments, millions. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`Secondary alignments`	read_count
\|\|	DRAGEN mapping	M Suppl'ry	Number of supplementary (chimeric) alignments, millions. A chimeric read is split over multiple loci (possibly due to structural variants). One alignment is referred to as the representative alignment, the other are supplementary	`Supplementary (chimeric) alignments`	read_count

Mapped / paired / duplicated

Distribution of reads based on pairing, duplication and mapping.

WGS Coverage Metrics

Coverage metrics over a region (where the region can be a target region, a QC coverage region, or the whole genome). Press the Help button for details.

The following criteria are used when calculating coverage:

Duplicate reads and clipped bases are ignored.
Only reads with MAPQ > min MAPQ and bases with BQ > min BQ are considered

Considering only bases usable for variant calling, i.e. excluding:

Clipped bases
Bases in duplicate reads
Reads with MAPQ < min MAPQ (default 20)
Bases with BQ < min BQ (default 10)
Reads with MAPQ = 0 (multimappers)
Overlapping mates are double-counted

Showing ¹²/₁₂ rows and ⁷/₁₄ columns.

Sample Name	M Aln reads	Mb Aln bases	Reads on target	M Reads on target	Bases on target	Mb Bases on target	Depth	Uniformity (>0.2×mean)	X cov	Y cov	MT cov	Mean aut cov	Med aut cov	Mean/med autosomal coverage
Sample-01	539.2	79625.9	100.0%	539.2	100.0%	79625.9	26.3 x	91.9 %	14.8 x	0.4 x	10570.9 x	27.9 x	29.0 x	0.96
Sample-02	637.9	94227.8	100.0%	637.9	100.0%	94227.8	31.1 x	91.9 %	17.5 x	0.5 x	12271.0 x	33.1 x	34.0 x	0.97
Sample-03	574.4	84815.4	100.0%	574.4	100.0%	84815.4	28.0 x	92.0 %	15.7 x	0.5 x	11158.5 x	29.8 x	31.0 x	0.96
Sample-04	548.8	81030.4	100.0%	548.8	100.0%	81030.4	26.7 x	91.9 %	15.0 x	0.4 x	10729.1 x	28.4 x	30.0 x	0.95
Sample-05	435.5	64308.2	100.0%	435.5	100.0%	64308.2	21.2 x	91.6 %	11.9 x	0.3 x	8918.2 x	22.6 x	23.0 x	0.98
Sample-06	505.8	74676.0	100.0%	505.8	100.0%	74676.0	24.6 x	92.1 %	13.8 x	0.4 x	9983.6 x	26.2 x	27.0 x	0.97
Sample-07	664.2	98033.1	100.0%	664.2	100.0%	98033.1	32.3 x	92.0 %	18.2 x	0.5 x	12056.5 x	34.4 x	36.0 x	0.96
Sample-08	674.2	99612.5	100.0%	674.2	100.0%	99612.5	32.8 x	92.0 %	18.6 x	0.5 x	12208.3 x	35.0 x	36.0 x	0.97
Sample-09	503.8	74449.2	100.0%	503.8	100.0%	74449.2	24.6 x	92.1 %	13.8 x	0.4 x	9682.0 x	26.1 x	27.0 x	0.97
Sample-10	502.3	74150.7	100.0%	502.3	100.0%	74150.7	24.4 x	92.0 %	13.8 x	0.5 x	9555.0 x	26.0 x	27.0 x	0.96
Sample-11	472.8	69910.6	100.0%	472.8	100.0%	69910.6	23.1 x	92.1 %	13.1 x	0.4 x	8578.9 x	24.5 x	25.0 x	0.98
Sample-12	461.8	68287.6	100.0%	461.8	100.0%	68287.6	22.5 x	92.0 %	12.8 x	0.3 x	8396.8 x	24.0 x	25.0 x	0.96

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

Sort	Group	Column	Description	ID	Scale
\|\|	DRAGEN coverage	M Aln reads	Total number of aligned reads.	`Aligned reads`	read_count
\|\|	DRAGEN coverage	Mb Aln bases	Total number of aligned bases.	`Aligned bases`	base_count
\|\|	DRAGEN coverage	Reads on target	% of uniquely mapped reads to region relative to the number of uniquely mapped reads to the genome. When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region.	`Aligned reads in genome pct`	None
\|\|	DRAGEN coverage	M Reads on target	Number of uniquely mapped reads to region relative to the number of uniquely mapped reads to the genome. When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region.	`Aligned reads in genome`	read_count
\|\|	DRAGEN coverage	Bases on target	% of uniquely mapped bases to the region relative to the number of uniquely mapped bases to the genome.	`Aligned bases in genome pct`	None
\|\|	DRAGEN coverage	Mb Bases on target	Number of uniquely mapped bases to the region relative to the number of uniquely mapped bases to the genome.	`Aligned bases in genome`	base_count
\|\|	DRAGEN coverage	Depth	Coverage depth over genome: number of uniquely mapped bases to genome divided by the number of sites in genome.	`Average alignment coverage over genome`	None
\|\|	DRAGEN coverage	Uniformity (>0.2×mean)	Percentage of sites with coverage greater than 20% of the mean coverage in region. Demonstrates the uniformity of coverage. The lower the better.	`Uniformity of coverage (PCT > 0.2*mean) over genome`	None
\|\|	DRAGEN coverage	X cov	Average chromosome X coverage over genome. Calculated as the number of bases that aligned to the chromosome X (or to the intersection of chromosome X with the target region) divided by the total number of loci in the chromosome X (or the intersection with the target region). If there is no chromosome X in the reference genome or the region does not intersect chromosome X, this metric shows as NA.	`Average chr X coverage over genome`	None
\|\|	DRAGEN coverage	Y cov	Average chromosome Y coverage over genome. Calculated as the number of bases that aligned to the chromosome Y (or to the intersection of chromosome Y with the target region) divided by the total number of loci in the chromosome Y (or the intersection with the target region). If there is no chromosome Y in the reference genome or the region does not intersect chromosome Y, this metric shows as NA.	`Average chr Y coverage over genome`	None
\|\|	DRAGEN coverage	MT cov	Average mitochondrial chromosome coverage over genome. Calculated as the number of bases that aligned to the mitochondrial chromosome (or to the intersection of mitochondrial chromosome with the target region) divided by the total number of loci in the mitochondrial chromosome (or the intersection with the target region). If there is no mitochondrial chromosome in the reference genome or the region does not intersect mitochondrial chromosome, this metric shows as NA.	`Average mitochondrial coverage over genome`	None
\|\|	DRAGEN coverage	Mean aut cov	Average autosomal coverage over genome. Calculated as the number of bases that aligned to the autosomal loci in genome divided by the total number of loci in the autosomal loci in genome. If there is no autosomes in the reference genome, or the region does not intersect autosomes, this metric shows as NA.	`Average autosomal coverage over genome`	None
\|\|	DRAGEN coverage	Med aut cov	Median alignment coverage over the autosomal loci in genome. If there is no autosome in the reference genome or the region does not intersect autosomes, this metric shows as NA.	`Median autosomal coverage over genome`	None
\|\|	DRAGEN coverage	Mean/med autosomal coverage	Mean autosomal coverage in genome divided by the median autosomal coverage in genome. If there is no autosome in the reference genome or the region does not intersect autosomes, this metric shows as NA.	`Mean/Median autosomal coverage ratio over genome`	None

Coverage distribution

Number of locations in the reference genome with a given depth of coverage.

Bases of a reference sequence (y-axis) are groupped by their depth of coverage (0×, 1×, …, N×) (x-axis). This plot shows the frequency of coverage depths relative to the reference sequence for each read dataset, which provides an indirect measure of the level and variation of coverage depth in the corresponding sequenced sample.

If reads are randomly distributed across the reference sequence, this plot should resemble a Poisson distribution (Lander & Waterman 1988), with a peak indicating approximate depth of coverage, and more uniform coverage depth being reflected in a narrower spread. The optimal level of coverage depth depends on the aims of the experiment, though it should at minimum be sufficiently high to adequately address the biological question; greater uniformity of coverage is generally desirable, because it increases breadth of coverage for a given depth of coverage, allowing equivalent results to be achieved at a lower sequencing depth (Sampson et al. 2011; Sims et al. 2014). However, it is difficult to achieve uniform coverage depth in practice, due to biases introduced during sample preparation (van Dijk et al. 2014), sequencing (Ross et al. 2013) and read mapping (Sims et al. 2014).

This plot may include a small peak for regions of the reference sequence with zero depth of coverage. Such regions may be absent from the given sample (due to a deletion or structural rearrangement), present in the sample but not successfully sequenced (due to bias in sequencing or preparation), or sequenced but not successfully mapped to the reference (due to the choice of mapping algorithm, the presence of repeat sequences, or mismatches caused by variants or sequencing errors). Related factors cause most datasets to contain some unmapped reads (Sims et al. 2014).

Cumulative coverage hist

Number of locations in the reference genome with at least given depth of coverage.

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.

Coverage per contig

Average coverage per contig or chromosome. Calculated as the number of bases (excluding duplicate marked reads, reads with MAPQ=0, and clipped bases), divided by the length of the contig or (if a target bed is used) the total length of the target region spanning that contig.

Coverage per contig (non-main)

Non-main contigs: unlocalized (random), unplaced (chrU), alts (*_alt), mitochondria (chrM), EBV, HLA. Zoom in to see more contigs as all labels don't fit the screen.

Fragment length hist

Distribution of estimated fragment lengths of mapped reads per read group. Only points supported by at least 5 reads are shown to prevent long flat tail. The plot is also smoothed down to showing 300 points on the X axis to reduce noise.

Trimmer Metrics

Metrics on trimmed reads.

Showing ¹²/₁₂ rows and ²²/₂₂ columns.

Sample Name	Total input reads	Total input bases	Total input bases R1	Total input bases R2	Average input read length	Total trimmed reads	Total trimmed bases	Remaining poly-G K-mers R1 3prime	Remaining poly-G K-mers R2 3prime	Poly-G soft trimmed reads unfiltered R1 3prime	Poly-G soft trimmed reads unfiltered R2 3prime	Poly-G soft trimmed reads filtered R1 3prime	Poly-G soft trimmed reads filtered R2 3prime	Poly-G soft trimmed bases unfiltered R1 3prime	Poly-G soft trimmed bases unfiltered R2 3prime	Poly-G soft trimmed bases filtered R1 3prime	Poly-G soft trimmed bases filtered R2 3prime	Total filtered reads	Reads filtered for minimum read length R1	Reads filtered for minimum read length R2
Sample-01	889538016.0	134320240416.0	67160120208.0	67160120208.0	151.0	0.0 (0.00%)	0.0 (0.00%)	11697424.0 (2.63%)	11153510.0 (2.51%)	15400466.0 (3.46%)	14202303.0 (3.19%)	0.0 (0.00%)	0.0 (0.00%)	1034660645.0 (1.54%)	797802943.0 (1.19%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-02	1248490238.0	188522025938.0	94261012969.0	94261012969.0	151.0	0.0 (0.00%)	0.0 (0.00%)	3316855.0 (0.53%)	3283579.0 (0.53%)	5886983.0 (0.94%)	5300255.0 (0.85%)	0.0 (0.00%)	0.0 (0.00%)	303842848.0 (0.32%)	253869225.0 (0.27%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-03	968011192.0	146169689992.0	73084844996.0	73084844996.0	151.0	0.0 (0.00%)	0.0 (0.00%)	12442700.0 (2.57%)	11879774.0 (2.45%)	16257044.0 (3.36%)	15329227.0 (3.17%)	0.0 (0.00%)	0.0 (0.00%)	1056885988.0 (1.45%)	844356061.0 (1.16%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-04	928400716.0	140188508116.0	70094254058.0	70094254058.0	151.0	0.0 (0.00%)	0.0 (0.00%)	14075231.0 (3.03%)	13487974.0 (2.91%)	18196005.0 (3.92%)	16825634.0 (3.62%)	0.0 (0.00%)	0.0 (0.00%)	1238268311.0 (1.77%)	964640155.0 (1.38%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-05	739121592.0	111607360392.0	55803680196.0	55803680196.0	151.0	0.0 (0.00%)	0.0 (0.00%)	16304159.0 (4.41%)	15530912.0 (4.20%)	19252068.0 (5.21%)	18558518.0 (5.02%)	0.0 (0.00%)	0.0 (0.00%)	1336899499.0 (2.40%)	1026954493.0 (1.84%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-06	871036592.0	131526525392.0	65763262696.0	65763262696.0	151.0	0.0 (0.00%)	0.0 (0.00%)	12843339.0 (2.95%)	12164644.0 (2.79%)	16503740.0 (3.79%)	15326031.0 (3.52%)	0.0 (0.00%)	0.0 (0.00%)	1104959377.0 (1.68%)	871492150.0 (1.33%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-07	1165431100.0	175980096100.0	87990048050.0	87990048050.0	151.0	0.0 (0.00%)	0.0 (0.00%)	15048049.0 (2.58%)	14419915.0 (2.47%)	18952855.0 (3.25%)	17843080.0 (3.06%)	0.0 (0.00%)	0.0 (0.00%)	1323121656.0 (1.50%)	1058974865.0 (1.20%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-08	1184034044.0	178789140644.0	89394570322.0	89394570322.0	151.0	0.0 (0.00%)	0.0 (0.00%)	11432771.0 (1.93%)	11493932.0 (1.94%)	13997788.0 (2.36%)	14678055.0 (2.48%)	0.0 (0.00%)	0.0 (0.00%)	1000515041.0 (1.12%)	890444033.0 (1.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-09	851048440.0	128508314440.0	64254157220.0	64254157220.0	151.0	0.0 (0.00%)	0.0 (0.00%)	9580044.0 (2.25%)	9321657.0 (2.19%)	12324836.0 (2.90%)	12081200.0 (2.84%)	0.0 (0.00%)	0.0 (0.00%)	785281791.0 (1.22%)	680203935.0 (1.06%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-10	881916822.0	133169440122.0	66584720061.0	66584720061.0	151.0	0.0 (0.00%)	0.0 (0.00%)	13964006.0 (3.17%)	13728700.0 (3.11%)	15399678.0 (3.49%)	15083248.0 (3.42%)	0.0 (0.00%)	0.0 (0.00%)	1056033701.0 (1.59%)	1046202213.0 (1.57%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-11	819733128.0	123779702328.0	61889851164.0	61889851164.0	151.0	0.0 (0.00%)	0.0 (0.00%)	8873796.0 (2.17%)	8529688.0 (2.08%)	11020906.0 (2.69%)	10507530.0 (2.56%)	0.0 (0.00%)	0.0 (0.00%)	664272868.0 (1.07%)	597554720.0 (0.97%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)
Sample-12	799838492.0	120775612292.0	60387806146.0	60387806146.0	151.0	0.0 (0.00%)	0.0 (0.00%)	6812934.0 (1.70%)	6483256.0 (1.62%)	9029066.0 (2.26%)	8412139.0 (2.10%)	0.0 (0.00%)	0.0 (0.00%)	498889638.0 (0.83%)	448767915.0 (0.74%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)	0.0 (0.00%)

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

Sort	Column	Description	ID	Scale
\|\|	Total input reads	Total input reads	`Total input reads`	None
\|\|	Total input bases	Total input bases	`Total input bases`	None
\|\|	Total input bases R1	Total input bases R1	`Total input bases R1`	None
\|\|	Total input bases R2	Total input bases R2	`Total input bases R2`	None
\|\|	Average input read length	Average input read length	`Average input read length`	None
\|\|	Total trimmed reads	Total trimmed reads	`Total trimmed reads`	None
\|\|	Total trimmed bases	Total trimmed bases	`Total trimmed bases`	None
\|\|	Average bases trimmed per read	Average bases trimmed per read	`Average bases trimmed per read`	None
\|\|	Average bases trimmed per trimmed read	Average bases trimmed per trimmed read	`Average bases trimmed per trimmed read`	None
\|\|	Remaining poly-G K-mers R1 3prime	Remaining poly-G K-mers R1 3prime	`Remaining poly-G K-mers R1 3prime`	None
\|\|	Remaining poly-G K-mers R2 3prime	Remaining poly-G K-mers R2 3prime	`Remaining poly-G K-mers R2 3prime`	None
\|\|	Poly-G soft trimmed reads unfiltered R1 3prime	Poly-G soft trimmed reads unfiltered R1 3prime	`Poly-G soft trimmed reads unfiltered R1 3prime`	None
\|\|	Poly-G soft trimmed reads unfiltered R2 3prime	Poly-G soft trimmed reads unfiltered R2 3prime	`Poly-G soft trimmed reads unfiltered R2 3prime`	None
\|\|	Poly-G soft trimmed reads filtered R1 3prime	Poly-G soft trimmed reads filtered R1 3prime	`Poly-G soft trimmed reads filtered R1 3prime`	None
\|\|	Poly-G soft trimmed reads filtered R2 3prime	Poly-G soft trimmed reads filtered R2 3prime	`Poly-G soft trimmed reads filtered R2 3prime`	None
\|\|	Poly-G soft trimmed bases unfiltered R1 3prime	Poly-G soft trimmed bases unfiltered R1 3prime	`Poly-G soft trimmed bases unfiltered R1 3prime`	None
\|\|	Poly-G soft trimmed bases unfiltered R2 3prime	Poly-G soft trimmed bases unfiltered R2 3prime	`Poly-G soft trimmed bases unfiltered R2 3prime`	None
\|\|	Poly-G soft trimmed bases filtered R1 3prime	Poly-G soft trimmed bases filtered R1 3prime	`Poly-G soft trimmed bases filtered R1 3prime`	None
\|\|	Poly-G soft trimmed bases filtered R2 3prime	Poly-G soft trimmed bases filtered R2 3prime	`Poly-G soft trimmed bases filtered R2 3prime`	None
\|\|	Total filtered reads	Total filtered reads	`Total filtered reads`	None
\|\|	Reads filtered for minimum read length R1	Reads filtered for minimum read length R1	`Reads filtered for minimum read length R1`	None
\|\|	Reads filtered for minimum read length R2	Reads filtered for minimum read length R2	`Reads filtered for minimum read length R2`	None

Time Metrics

Time metrics for DRAGEN run. Total run time is less than the sum of individual steps because of parallelization.

DRAGEN-FastQc

DRAGEN-FastQc is a Bio-IT Platform that provides ultra-rapid secondary analysis of sequencing data using field-programmable gate array technology (FPGA).

Per-Position Quality Score Ranges

The range of quality value across each base position in each sample or read

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

Per-Position Mean Quality Scores

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

Per-Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help: The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

Sequence Length Distribution

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

Per-Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help: This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content. In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution. An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

GC Content Mean Quality Scores

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

Per-Position N Content

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

From the FastQC help: If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called. It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

Per-Position Sequence Content

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

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor. To see the data as a line plot, as in the original FastQC graph, click on a sample track. From the FastQC help: Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called. In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other. It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

Bismark

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

M-Bias

This plot shows the average percentage methylation and coverage across reads. See the bismark user guide for more information on how these numbers are generated.

v1.12.dev0

MultiQC Toolbox

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DRAGEN

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WGS Coverage Metrics

Coverage distribution

Cumulative coverage hist

Coverage per contig

Coverage per contig (non-main)

Fragment length hist

Trimmer Metrics

Time Metrics

DRAGEN-FastQc

Per-Position Quality Score Ranges

Per-Position Mean Quality Scores

Per-Sequence Quality Scores

Sequence Length Distribution

Per-Sequence GC Content

GC Content Mean Quality Scores

Per-Position N Content

Per-Position Sequence Content

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Adapter Content

Bismark

M-Bias

Toggle navigation v1.12.dev0

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General Statistics: Columns

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Table Kehn: Columns

Mapped / paired / duplicated

WGS Coverage Metrics Help

Table Cdjq: Columns

Coverage distribution Help

Cumulative coverage hist Help

Coverage per contig

Coverage per contig (non-main)

Fragment length hist

Trimmer Metrics

Table Kvny: Columns

Time Metrics

DRAGEN-FastQc

Per-Position Quality Score Ranges

Per-Position Mean Quality Scores Help

Per-Sequence Quality Scores Help

Sequence Length Distribution

Per-Sequence GC Content Help

GC Content Mean Quality Scores Help

Per-Position N Content Help

Per-Position Sequence Content Help

Rollover for sample name

Adapter Content Help

Bismark

M-Bias

v1.12.dev0

Highlight Samples

Rename Samples

Show / Hide Samples

WGS Coverage Metrics

Coverage distribution

Cumulative coverage hist

Per-Position Mean Quality Scores

Per-Sequence Quality Scores

Per-Sequence GC Content

GC Content Mean Quality Scores

Per-Position N Content

Per-Position Sequence Content

Adapter Content