NGS reports exp mixed_yri_mx2

Experiment info

This report was generated by genomecomb version 0.106.0. It combines overview results on 3 samples of experiment mixed_yri_mx2

Yield and quality overview

#	sample	numreads	numbases-mb	pct-unique-reads	fw-qual-mean	fw-qual-stdev	rev-qual-mean	rev-qual-stdev
1	exNA19239mx2	2444	0.239974	83.14	37.5556	4.0644	36.9906	4.7998
2	exNA19240mx2	1634	0.15966	92.41	37.3868	4.2164	36.8146	5.0853
3	gilNA19240mx2	19894	1.931757	99.93	38.1249	4.0545	38.6194	2.8907

Alignment overview

#	sample	alignment	numalignments	numreads	mapped-reads	pct_mapped-reads	duplicate-reads	properly-paired-reads	num-mapped-bases-mb	pct-mapped-bases	pct-mapped-ontarget
1	exNA19239mx2	rdsbwa	2444	2444	2444	100.00	412	2444	0.239974	99.98	55.56
2	exNA19240mx2	rdsbwa	1634	1634	1634	100.00	124	1634	0.15966	99.97	63.80
3	gilNA19240mx2	rdsbwa	19894	19894	19894	100.00	14	19894	1.931757	99.95	0.00

Alignment target overview

no target region was supplied for rdsbwa-gilNA19240mx2. The full "sequenced genome" region in /complgen/refseq/hg19/extra/reg_hg19_sequencedgenome.tsv.zst was used as target region for calulations in the table

#	sample	alignment	target-region-mb	pct-target-1X	pct-target-2X	pct-target-10X	pct-target-20X	pct-target-30X
1	exNA19239mx2	rdsbwa	64.190747	0.0082	0.0082	0.0078	0.0057	0.0026
2	exNA19240mx2	rdsbwa	64.190747	0.0082	0.0082	0.0073	0.0035	0.0013
3	gilNA19240mx2	rdsbwa	2897.310566	0.0017	0.0017	0.0017	0.0017	0.0015

Variants overview

#	sample	alignment	varcaller	vars	qvars	qvars-zyg-m	qvars-zyg-t	qvars-TiTv-ratio
1	exNA19239mx2	rdsbwa	gatkh	12	5	2	3	4.00
2	exNA19239mx2	rdsbwa	strelka	11	5	2	3	4.00
3	exNA19240mx2	rdsbwa	gatkh	9	4	2	2	3.00
4	exNA19240mx2	rdsbwa	strelka	9	4	2	2	3.00
5	gilNA19240mx2	rdsbwa	gatkh	112	110	24	82	2.91
6	gilNA19240mx2	rdsbwa	strelka	106	102	24	74	2.82

Gender prediction overview

#	sample	predicted-gender	Y-over-X-ratio	normalised-Y-over-X-ratio	pct-heterozygous-Y
1	exNA19239mx2	u	?	?	?
2	exNA19240mx2	u	?	?	?
3	gilNA19240mx2	u	?	?	?

Number of on-target bases with given depth

Number of off-target bases with given depth

fastqc overview

#	sample	dir	gc	per-base-quality	per-sequence-quality	per-base-content	per-sequence-gc	per-base-N	length-distribution	sequence-duplication	overrepresented-seq
1	exNA19239mx2	forward	53	pass	pass	warn	fail	pass	warn	pass	warn
2	exNA19239mx2	reverse	53	pass	pass	warn	fail	pass	warn	pass	warn
3	exNA19240mx2	forward	53	pass	pass	pass	fail	pass	warn	pass	warn
4	exNA19240mx2	reverse	53	pass	pass	warn	fail	pass	warn	pass	warn
5	gilNA19240mx2	forward	48	pass	pass	pass	warn	pass	warn	pass	pass
6	gilNA19240mx2	reverse	48	pass	pass	pass	fail	pass	warn	pass	pass

NGS reports exp mixed_yri_mx2

Experiment info

Yield and quality overview

Alignment overview

Alignment target overview

Variants overview

Gender prediction overview

Number of on-target bases with given depth

Number of off-target bases with given depth

fastqc overview

Fastqc forward read quality per position (median and 10th percentile)

Fastqc reverse read quality per position (median and 10th percentile)

Fastqc forward reads per quality

Fastqc reverse reads per quality

Fastqc forward reads GC content

Fastqc reverse reads GC content

Fastqc forward reads length distribution

Fastqc reverse reads length distribution

Quality distribution

Readlength distribution