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Some more fake QC data
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@davmlaw
davmlaw committed Jul 17, 2024
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40 changes: 40 additions & 0 deletions ...xome/Exome_20_022_200920_NB501009_0410_AHNLYFBGXG/4_QC/exec_stats/hiseq_sample2_stats.tsv
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Name Value
Sample hiseq_sample2
%Reads 4.32
Reads 2520760.00
DedupReads 3365107.00
%ReadEnrich 83.28
MedianInsert 361.00
%bp20x_Kit 96.35
MeanDepth_Kit 154.43
%Duplication 5.42
%UniformCov 93.39
SNPs 363.00
%SNPs_dbSNP 96.62
Indels 923.00
%Indels_dbSNP 95.75
Ts/Tv 2.25
VCFx_hetero 0.00
VCFx_homo 32.00
VCF_HetHom_ratio 0.00
%VCFx_homo 100.00
BAM_y_reads 0.00
BAM_x_reads 66474.00
BAM_ratio 0.00
BAM_sex F
BAM_sex_comment Female < 0.01
VCF_sex M
VCF_sex_comment Male < 0.9
SampleID_LOD 16.60
%map2diff_chr 0.75
%SoftClipRate 0.02
%ErrorRate 0.6
Nb_genes_original_GOI 1
Nb_genes_final_GOI 1
Nb_unrecognized_genes_GOI 0
MeanDepth_GOI 350.84
%bp20X_GOI 100.00
%bp10X_GOI 100.00
Nb_low_coverage_exons_GOI 0
Nb_low_coverage_exons_Kit 50
SexMatch M=yes
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153 changes: 153 additions & 0 deletions ...Focus_20_001_200626_NB501009_0391_AHFHLJBGXG/4_QC/exec_stats/miseq_sample1_qc_summary.txt
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Version 0.1.0
Date run 20/01/2016
Sample miseq_sample1

Observed Range in reference standard
% of bases with >20x coverage across GOI 35.86
% of bases with >10x coverage across GOI 69.08
Mean coverage across GOI 17.56 135.24 - 314.39
Mean coverage across kit 18.56 148.00 - 354.40
Uniformity of Coverage 94.01 96.27 - 96.98
Read enrichment (%) 22.30 58.56 - 78.70
Duplicated alignable reads 8.16 4.28 - 5.36
Mean insert 293.00 232.55 - 295.70
Ts/Tv 2.898 2.78 - 2.94
Number SNPs 8691 9197.35 - 9572.70
%SNPs in dbSNP 98.60 97.27 - 98.76
Number indels 522 836.60 - 894.70
%indels in dbSNP 80.65 66.77 - 69.87

GOI with less than 100% of bases having at least 20x coverage
1. In sample but not in reference standard

Gene Transcript Exon Coordinate Min coverage Mean coverage Mean (reference standard) % bases >20x % bases <10x % bases @ 0x Estimated Sensitivity of Detection
SOX2 NM_003106 Chr3:181430148:181431102 3 25.12 292.00 81.45 5.77 0.00 0.96
TFAP2A NM_003220 Chr6:10398649:10398938 1 9.01 158.36 0.00 40.83 0.00 0.75
TFAP2A NM_003220 Chr6:10400680:10400822 5 10.94 144.93 0.00 19.72 0.00 0.91
TFAP2A NM_003220 Chr6:10402724:10402843 8 11.13 119.48 0.00 21.01 0.00 0.92
TFAP2A NM_003220 Chr6:10404740:10404972 2 6.44 134.73 0.00 98.71 0.00 0.73
TFAP2A NM_003220 Chr6:10407025:10407077 8 9.12 94.04 0.00 65.38 0.00 0.88
TFAP2A NM_003220 Chr6:10415173:10415218 6 7.91 125.68 0.00 100.00 0.00 0.84
GJA1 NM_000165 Chr6:121767993:121769142 11 42.83 407.28 94.34 0.00 0.00 0.98
HCCS NM_001122608 ChrX:11130180:11130280 5 10.78 230.55 0.00 27.00 0.00 0.90
HCCS NM_001122608 ChrX:11132954:11133106 4 6.25 158.74 0.00 100.00 0.00 0.75
HCCS NM_001122608 ChrX:11135386:11135535 10 14.49 260.69 0.00 0.00 0.00 0.97
HCCS NM_001122608 ChrX:11136620:11136740 9 12.06 230.50 0.00 2.50 0.00 0.94
HCCS NM_001122608 ChrX:11139026:11139113 6 6.39 197.93 0.00 100.00 0.00 0.78
HCCS NM_001122608 ChrX:11139731:11139930 8 13.18 251.90 0.00 3.52 0.00 0.95
BCOR NM_001123385 ChrX:39911361:39911653 10 17.81 336.60 36.30 0.00 0.00 0.97
BCOR NM_001123385 ChrX:39913138:39913295 7 10.07 140.75 0.00 33.12 0.00 0.90
BCOR NM_001123385 ChrX:39913508:39913586 11 13.45 238.79 0.00 0.00 0.00 0.96
BCOR NM_001123385 ChrX:39914620:39914766 9 12.42 308.39 0.00 0.68 0.00 0.95
BCOR NM_001123385 ChrX:39916407:39916574 10 20.26 253.79 65.87 0.00 0.00 0.97
BCOR NM_001123385 ChrX:39921391:39921646 3 6.08 180.25 0.00 100.00 0.00 0.73
BCOR NM_001123385 ChrX:39922860:39923205 15 31.57 353.79 89.86 0.00 0.00 0.98
BCOR NM_001123385 ChrX:39923588:39923852 17 21.88 314.28 97.35 0.00 0.00 0.98
BCOR NM_001123385 ChrX:39930225:39930412 3 10.58 246.89 0.00 38.50 0.00 0.89
BCOR NM_001123385 ChrX:39930889:39930943 4 6.80 81.94 0.00 100.00 0.00 0.76
BCOR NM_001123385 ChrX:39935706:39935785 4 5.80 133.70 0.00 100.00 0.00 0.74
BCOR NM_001123385 ChrX:39937096:39937182 9 11.26 159.51 0.00 2.33 0.00 0.93
NAA10 NM_003491 ChrX:153195439:153195676 2 7.87 169.93 0.00 68.78 0.00 0.79
NAA10 NM_003491 ChrX:153196215:153196300 4 5.34 167.19 0.00 100.00 0.00 0.68
NAA10 NM_003491 ChrX:153197523:153197568 0 0.00 70.65 0.00 100.00 100.00 0.00
NAA10 NM_003491 ChrX:153197768:153197884 4 8.45 154.21 0.00 48.28 0.00 0.84
NAA10 NM_003491 ChrX:153197991:153198037 6 6.89 140.85 0.00 100.00 0.00 0.80
NAA10 NM_003491 ChrX:153199395:153199454 10 11.19 178.87 0.00 0.00 0.00 0.93
NAA10 NM_003491 ChrX:153199829:153199928 7 9.94 228.80 0.00 44.44 0.00 0.90
KAT6B NM_012330 Chr10:76719727:76719836 4 9.34 108.85 0.00 43.12 0.00 0.88
KAT6B NM_012330 Chr10:76729417:76729533 6 8.94 138.78 0.00 59.48 0.00 0.87
KAT6B NM_012330 Chr10:76729777:76729859 14 15.63 155.54 0.00 0.00 0.00 0.98
KAT6B NM_012330 Chr10:76737073:76737195 2 2.19 131.36 0.00 100.00 0.00 0.05
KAT6B NM_012330 Chr10:76738981:76739097 6 11.28 112.63 0.00 12.93 0.00 0.92
KAT6B NM_012330 Chr10:76748776:76748870 10 12.50 109.13 0.00 0.00 0.00 0.95
KAT6B NM_012330 Chr10:76780339:76780571 4 7.63 131.04 0.00 85.34 0.00 0.82
KAT6B NM_012330 Chr10:76780883:76781043 5 10.20 145.57 0.00 38.75 0.00 0.89
KAT6B NM_012330 Chr10:76781638:76781989 6 13.79 174.42 2.56 11.40 0.00 0.94
KAT6B NM_012330 Chr10:76784715:76785007 2 6.93 113.57 0.00 95.55 0.00 0.75
KAT6B NM_012330 Chr10:76788246:76790804 5 31.25 320.49 80.41 2.50 0.00 0.97
YAP1 NM_001130145 Chr11:101984874:101985125 7 14.91 177.08 0.00 1.59 0.00 0.97
YAP1 NM_001130145 Chr11:102033186:102033302 4 4.83 70.23 0.00 100.00 0.00 0.64
YAP1 NM_001130145 Chr11:102056748:102056862 0 5.55 72.51 0.00 100.00 0.88 0.66
YAP1 NM_001130145 Chr11:102076623:102076805 3 8.34 127.52 0.00 64.29 0.00 0.80
YAP1 NM_001130145 Chr11:102080247:102080295 6 9.27 142.31 0.00 43.75 0.00 0.88
YAP1 NM_001130145 Chr11:102094352:102094483 5 7.98 99.30 0.00 91.60 0.00 0.83
YAP1 NM_001130145 Chr11:102098199:102098312 1 2.60 91.59 0.00 100.00 0.00 0.21
YAP1 NM_001130145 Chr11:102100432:102100671 11 15.43 217.50 0.00 0.00 0.00 0.97
BMP4 NM_130850 Chr14:54416749:54417606 5 25.42 279.09 70.83 7.82 0.00 0.96
BMP4 NM_130850 Chr14:54418570:54418940 3 12.94 148.50 19.19 35.95 0.00 0.90
OTX2 NM_021728 Chr14:57268452:57269073 5 15.10 202.74 30.43 27.70 0.00 0.93
OTX2 NM_021728 Chr14:57270905:57271081 3 5.71 77.39 0.00 100.00 0.00 0.69
OTX2 NM_021728 Chr14:57272077:57272174 10 12.97 162.00 0.00 0.00 0.00 0.95
STRA6 NM_001199042 Chr15:74473122:74473278 3 11.08 108.87 0.00 30.13 0.00 0.87
STRA6 NM_001199042 Chr15:74473635:74473799 10 18.12 204.14 46.34 0.00 0.00 0.97
STRA6 NM_001199042 Chr15:74474501:74474603 10 12.16 215.75 0.00 0.00 0.00 0.94
STRA6 NM_001199042 Chr15:74474683:74474801 6 11.62 177.47 0.00 33.05 0.00 0.92
STRA6 NM_001199042 Chr15:74476196:74476330 8 10.49 141.59 0.00 20.15 0.00 0.91
STRA6 NM_001199042 Chr15:74477320:74477396 6 7.86 123.15 0.00 69.74 0.00 0.83
STRA6 NM_001199042 Chr15:74481455:74481618 1 3.75 95.62 0.00 100.00 0.00 0.43
STRA6 NM_001199042 Chr15:74483180:74483242 11 14.85 205.38 0.00 0.00 0.00 0.97
STRA6 NM_001199042 Chr15:74483507:74483584 15 18.30 215.92 25.97 0.00 0.00 0.98
STRA6 NM_001199042 Chr15:74483764:74483832 14 16.22 205.73 2.94 0.00 0.00 0.98
STRA6 NM_001199042 Chr15:74486140:74486263 6 7.61 103.16 0.00 92.68 0.00 0.83
STRA6 NM_001199042 Chr15:74487642:74487809 6 10.76 134.95 0.00 31.14 0.00 0.90
STRA6 NM_001199042 Chr15:74487992:74488016 10 11.08 151.48 0.00 0.00 0.00 0.92
STRA6 NM_001199042 Chr15:74488348:74488488 5 7.76 157.11 0.00 100.00 0.00 0.83
STRA6 NM_001199042 Chr15:74489678:74489764 5 9.65 139.17 0.00 50.00 0.00 0.88
STRA6 NM_001199042 Chr15:74490092:74490159 9 12.76 126.29 0.00 5.97 0.00 0.95
STRA6 NM_001199042 Chr15:74494495:74494623 11 12.71 192.78 0.00 0.00 0.00 0.95
STRA6 NM_001199042 Chr15:74494758:74494860 5 9.69 150.11 0.00 36.27 0.00 0.87

2. In sample and in reference standard:

Gene Transcript Exon Coordinate Min coverage Mean coverage Mean (reference standard) % bases >20x % bases <10x % bases @ 0x Estimated Sensitivity of Detection
TFAP2A NM_003220 Chr6:10410133:10410568 1 14.12 135.09 31.26 26.90 0.00 0.85
BCOR NM_001123385 ChrX:39921998:39922324 0 3.22 92.90 0.00 100.00 0.92 0.34
BCOR NM_001123385 ChrX:39931601:39934433 0 19.57 319.19 51.69 16.24 0.04 0.92
NAA10 NM_003491 ChrX:153200336:153200357 0 0.00 16.48 0.00 100.00 100.00 0.00
KAT6B NM_012330 Chr10:76602615:76603236 3 39.43 342.22 80.68 9.18 0.00 0.94
KAT6B NM_012330 Chr10:76735156:76736088 1 4.89 70.68 0.00 100.00 0.00 0.58
YAP1 NM_001130145 Chr11:101981579:101981900 1 6.88 119.04 0.00 66.04 0.00 0.65

Genes tested: Total = 12
RARB,OTX2,NAA10,BMP4,TFAP2A,STRA6,BCOR,HCCS,YAP1,KAT6B,SOX2,GJA1
Genes with omitted alternate haplotypes:

Low complexity
Transcript Exon Low_complexity_start:low_complexity_end Low_complexity_sequence Low_complexity_length
SOX2:NM_003106 chr3:181430148:181431102 181430204:181430218 GGC 12
BCOR:NM_001123385 chrX:39913508:39913586 39913603:39913612 A 7
BCOR:NM_001123385 chrX:39930225:39930412 39930432:39930447 A 13
BCOR:NM_001123385 chrX:39931601:39934433 39931588:39931597 G 7
KAT6B:NM_012330 chr10:76735156:76736088 76735893:76735907 CTC 12
KAT6B:NM_012330 chr10:76741544:76741686 76741701:76741710 A 7
KAT6B:NM_012330 chr10:76781638:76781989 76781905:76781928 AAG 21
KAT6B:NM_012330 chr10:76781638:76781989 76781833:76781847 AGG 12
KAT6B:NM_012330 chr10:76781638:76781989 76781904:76781930 GAA 24
KAT6B:NM_012330 chr10:76781638:76781989 76781832:76781846 GAG 12
KAT6B:NM_012330 chr10:76788246:76790804 76788210:76788220 T 8
KAT6B:NM_012330 chr10:76788246:76790804 76788689:76788703 AAG 12
KAT6B:NM_012330 chr10:76788246:76790804 76788644:76788661 AGG 15
KAT6B:NM_012330 chr10:76788246:76790804 76788688:76788702 GAA 12
KAT6B:NM_012330 chr10:76788246:76790804 76788643:76788660 GAG 15
YAP1:NM_001130145 chr11:102056748:102056862 102056721:102056738 T 15
YAP1:NM_001130145 chr11:102076623:102076805 102076599:102076611 T 10
YAP1:NM_001130145 chr11:102080247:102080295 102080324:102080336 A 10
STRA6:NM_001199042 chr15:74494495:74494623 74494641:74494652 A 9

###############################################################

Description of terms
# All ranges are from the 5th to the 95th percentile
# Mean coverage across GOI: ref range for GOI (per sample) only. Defaults to transcript with most bases if transcript not specified
# Mean coverage across kit: all genes from vendor specified bed
# Uniformity of Coverage: % of bases at at least 20% of the mean depth
# Read enrichment (%): reads on target
# Duplicated alignable reads: PCR duplicated reads
# Mean insert: distance between read pairs
# Ts/Tv: transition/transversion - 3 is ideal

###############################################################

Program versions


40 changes: 40 additions & 0 deletions ...s/GMPFocus_20_001_200626_NB501009_0391_AHFHLJBGXG/4_QC/exec_stats/miseq_sample1_stats.tsv
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Name Value
Sample miseq_sample1
%Reads 5.32
Reads 520760.00
DedupReads 365107.00
%ReadEnrich 54.28
MedianInsert 153.00
%bp20x_Kit 98.35
MeanDepth_Kit 201.43
%Duplication 3.42
%UniformCov 84.69
SNPs 363.00
%SNPs_dbSNP 96.62
Indels 923.00
%Indels_dbSNP 95.75
Ts/Tv 2.1
VCFx_hetero 0.00
VCFx_homo 39.00
VCF_HetHom_ratio 0.00
%VCFx_homo 100.00
BAM_y_reads 0.00
BAM_x_reads 6474.00
BAM_ratio 0.00
BAM_sex F
BAM_sex_comment Female < 0.01
VCF_sex M
VCF_sex_comment Male < 0.9
SampleID_LOD 16.60
%map2diff_chr 0.75
%SoftClipRate 0.02
%ErrorRate 0.36
Nb_genes_original_GOI 1
Nb_genes_final_GOI 1
Nb_unrecognized_genes_GOI 0
MeanDepth_GOI 162.84
%bp20X_GOI 100.00
%bp10X_GOI 100.00
Nb_low_coverage_exons_GOI 0
Nb_low_coverage_exons_Kit 50
SexMatch M=yes
27 changes: 27 additions & 0 deletions ...s/GMPFocus_20_001_200626_NB501009_0391_AHFHLJBGXG/4_QC/exec_stats/miseq_sample1_stats.txt
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Sample miseq_sample1 Gold
%bp20x_GOI 100.00
%bp10x_GOI 100.00
MeanDepth_GOI 262.84 211.83 - 324.80
MeanDepth_Kit 264.34 > 100x
%UniformCov 97.66 98.17 - 98.58
%ReadEnrich 89.02 87.72 - 91.76
%Duplication 10.07 5.90 - 11.82
MedianInsert 247 225 - 264
Ts/Tv 2.60 2.60 - 2.81
SNPs 3685 3515 - 3825
%SNPs_dbSNP 97.39 96.44 - 98.69
Indels 505 457 - 506
%Indels_dbSNP 63.37 61.30 - 66.63
SexMatch M=yes
VCFsex M
VCFratio 0.24
VCFx_homo 82
VCFx_hetero 20
VCFsexComment Male < 0.9
BAMsex M
BAMx_reads 650814
BAMy_reads 21227
BAMratio 30.00
BAMsexComment chX/chrY reads ratio=30(< 100)
SampleID_LOD 19.75
GOIs 2
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