-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathWTEST_achab.html
More file actions
4657 lines (3896 loc) · 189 KB
/
WTEST_achab.html
File metadata and controls
4657 lines (3896 loc) · 189 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>WTEST_ Achab catch</title>
<script type="text/javascript" language="javascript" src='https://code.jquery.com/jquery-3.5.1.js'></script>
<script type="text/javascript" language="javascript" src='https://cdn.datatables.net/1.10.22/js/jquery.dataTables.min.js'></script>
<script type="text/javascript" language="javascript" src='https://cdn.datatables.net/fixedheader/3.1.7/js/dataTables.fixedHeader.min.js'></script>
<script>
var filter;
$(document).ready(function () {
$('#table thead tr').clone(true).appendTo( '#table thead' );
$('#table thead tr:eq(1) th').each( function (i) {
var title = $(this).text();
$(this).html( '<input type="text" placeholder="Search" />' );
$(this).removeClass('rotate').off('click');
$( 'input', this ).on( 'keyup change', function () {
if ( table.column(i).search() !== this.value ) {
table
.column(i)
.search( this.value )
.draw();
}
} );
} );
var table = $('#table').DataTable( {"dom": 'ift', "order": [] ,"lengthMenu":[ [ -1 ],[ "All" ]], "fixedHeader": true, "orderCellsTop": true, "oLanguage": {"sInfo": "TOTAL: _TOTAL_ lines" } } );
filter = function (evt, cat) {
var metadata = document.getElementsByClassName("META");
if (cat === "META"){
document.getElementById("ALL").style.visibility = "collapse";
for (i = 0; i < metadata.length; i++) {
metadata[i].style.display = "block";
}
}else{
for (i = 0; i < metadata.length; i++) {
metadata[i].style.display = "none";
}
document.getElementById("ALL").style.visibility = "visible";
var rowunselected = document.getElementsByTagName("TR");
for (i = 0; i < rowunselected.length; i++) {
rowunselected[i].style.visibility = "collapse";
}
var rowhead = document.getElementById('table').getElementsByClassName('head');
for (i = 0; i < rowhead.length; i++) {
rowhead[i].style.visibility = "visible";
}
var rowselect = document.getElementById('table').getElementsByClassName(cat);
for (i = 0; i < rowselect.length; i++) {
rowselect[i].style.visibility = "visible";
}
}
var tablinks = document.getElementsByClassName("tablinks");
for (i = 0; i < tablinks.length; i++) {
tablinks[i].className = tablinks[i].className.replace(" active", "");
}
evt.currentTarget.className += " active";
window.scrollTo(1, 0);
/* $('#ALL').DataTable().fixedHeader.adjust(); */
}
/*double click on favorite row*/
$('#table tbody').on('dblclick', 'tr', function () {
this.classList.toggle('favorite');
} );
});
</script>
<link rel="stylesheet" type="text/css" href='https://cdn.datatables.net/1.10.22/css/jquery.dataTables.min.css'>
<link rel="stylesheet" type="text/css" href='https://cdn.datatables.net/fixedheader/3.1.7/css/fixedHeader.dataTables.min.css'>
<style>
/* Style the tab */
.tab {
overflow: hidden;
border: 1px solid #ccc;
background-color: #f1f1f1;
left: 0;
bottom: 0;
position: fixed;
position: -webkit-sticky;
position: sticky;
}
/* Style the buttons inside the tab */
.tab input {
background-color: inherit;
float: left;
border: none;
outline: none;
cursor: pointer;
padding: 14px 16px;
transition: 0.3s;
font-size: 17px;
}
/* Change background color of buttons on hover */
.tab input:hover {
background-color: #ddd;
}
/* Create an active/current tablink class */
.tab input.active {
background-color: #ccc;
}
/* .tab input:focus {
background-color: #ccc;
}*/
#ALL tbody tr.favorite{
background-color: goldenrod;
}
#ALL tbody tr:hover{
background-color: teal;
}
#ALL tbody tr td div{
max-height: 45px;
text-overflow : ellipsis;
-o-text-overflow: ellipsis;
-ms-text-overflow: ellipsis;
-moz-binding: url('ellipsis.xml#ellipsis');
overflow: hidden;
white-space: nowrap;
}
#ALL tbody tr td div:hover{
overflow: visible;
white-space : pre-line;
overflow-wrap : break-word;
}
td {
text-align: center;
}
/*rotate header*/
thead input {
width: 100%;
}
th.rotate {
height: 150px;
white-space: nowrap;
}
th.rotate > div {
transform:
translate(25px, 51px)
rotate(315deg);
width: 30px;
}
th.rotate > div > span {
/*border-bottom: 1px solid #ccc;*/
padding: 5px 10px;
}
/* Style METADATA */
.META {
display: none;
white-space: pre-line;
}
/* Style the tab content */
.tabcontent {
visibility: visible;
padding: 6px 12px;
/*border: 1px solid #ccc;*/
border-top: none;
}
/* Style the tooltip div */
.tooltip {
position: relative;
display: inline-block;
/*border-bottom: 1px dotted black;*/
max-width: 120px;
word-wrap: break-word;
}
.tooltip .tooltiptext {
visibility: hidden;
width: auto;
min-width: 300px;
max-width: 600px;
height: auto;
background-color: #555;
color: #fff;
text-align: left;
border-radius: 6px;
padding: 5px 0;
position: absolute;
z-index: 1;
top: 100%;
left: 20%;
margin-left: -20px;
opacity: 0;
transition: opacity 0.3s;
overflow: hidden;
text-overflow: ellipsis;
white-space: pre-line;
overflow-wrap: break-word;
}
.tooltip:hover .tooltiptext {
visibility: visible;
opacity: 1;
}
</style>
</head>
<body><div class="META"><b>Arguments:</b><br>--vcf INPUT_hg19_multianno_MPA.vcf --outPrefix WTEST --candidates candid.txt --trio --case B00GMSH --dad B00GMSI --mum B00GMSJ <br><br><br><b>VCF Header:</b><br>##fileformat=VCFv4.2
##GATKCommandLine.HaplotypeCaller=ID=HaplotypeCaller,Version=3.8-0-ge9d806836,Date="Wed Aug 01 04:38:56 CEST 2018",Epoch=1533091136036,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/MERGED_SAMPLES.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/HaplotypeCaller-1-sg/temp_01_of_28/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false out=/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/HaplotypeCaller-1-sg/temp_01_of_28/MERGED_SAMPLES.raw.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/home/guignardt/work-mobidic/nenufaar/refData/dbSNP/138/CORRECT_dbsnp_138.hg19.vcf.gz) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ReadPosRankSumTest] excludeAnnotation=[] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=10 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=1 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
##GATKCommandLine.VariantFiltration=ID=VariantFiltration,Version=3.8-0-ge9d806836,Date="Wed Aug 01 05:16:32 CEST 2018",Epoch=1533093392176,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/VariantFiltration-1-sg/temp_01_of_28/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/MERGED_SAMPLES.raw.polyx.vcf) mask=(RodBinding name= source=UNBOUND) out=/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/VariantFiltration-1-sg/temp_01_of_28/MERGED_SAMPLES.raw.polyx.gatk.vcf filterExpression=[DP 20, QUAL 30.0, QD 1.5, FS 60.000, MQ 10.00, POLYX 7] filterName=[LowCoverage, LowQual, LowQD, StrandBias, LowMappingQuality, R8] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
##VCFPolyXCmdLine=-R /home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.fa -o output/28658/AJI_Fam8/MERGED_SAMPLES/559/MERGED_SAMPLES.raw.polyx.vcf output/28658/AJI_Fam8/MERGED_SAMPLES/559/MERGED_SAMPLES.raw.vcf
##VCFPolyXHtsJdkHome=lib/com/github/samtools/htsjdk/2.6.1/htsjdk-2.6.1.jar
##VCFPolyXHtsJdkVersion=2.6.1
##VCFPolyXVersion=ff2326c651be81dd8b99173a69d6005b274ca4c6
##bcftools_normCommand=norm -O v -m - -o /mnt/data/MobiDL/captainAchab/Done/B00GMSH/CaptainAchab/B00GMSH.vcf /home/adminngs/autoAchab/cromwell-executions/captainAchab/125ed6dd-2cf6-417a-8456-32f4c307d094/call-bcftoolsNorm/inputs/-793930549/B00GMSH_leftalign.vcf; Date=Fri Jul 3 15:39:50 2020
##bcftools_normVersion=1.9+htslib-1.9
##reference=file:///home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.fa
##INFO=ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"
##INFO=ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"
##INFO=ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"
##INFO=ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"
##INFO=ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"
##INFO=ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"
##INFO=ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"
##INFO=ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"
##INFO=ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"
##INFO=ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"
##INFO=ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"
##INFO=ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"
##INFO=ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"
##INFO=ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"
##INFO=ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"
##INFO=ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"
##INFO=ID=POLYX,Number=1,Type=Integer,Description="Number of repeated bases around REF"
##INFO=ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"
##INFO=ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"
##INFO=ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"
##INFO=ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"
##INFO=ID=Func.refGene,Number=.,Type=String,Description="Func.refGene annotation provided by ANNOVAR"
##INFO=ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR"
##INFO=ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR"
##INFO=ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR"
##INFO=ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR"
##INFO=ID=Approved_name.refGene,Number=.,Type=String,Description="Approved_name.refGene annotation provided by ANNOVAR"
##INFO=ID=Phenotypes.refGene,Number=.,Type=String,Description="Phenotypes.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_upper_rank.refGene,Number=.,Type=String,Description="oe_lof_upper_rank.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_upper_bin.refGene,Number=.,Type=String,Description="oe_lof_upper_bin.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof.refGene,Number=.,Type=String,Description="oe_lof.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_lower.refGene,Number=.,Type=String,Description="oe_lof_lower.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_upper.refGene,Number=.,Type=String,Description="oe_lof_upper.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_mis.refGene,Number=.,Type=String,Description="oe_mis.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_mis_lower.refGene,Number=.,Type=String,Description="oe_mis_lower.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_mis_upper.refGene,Number=.,Type=String,Description="oe_mis_upper.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_syn.refGene,Number=.,Type=String,Description="oe_syn.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_syn_lower.refGene,Number=.,Type=String,Description="oe_syn_lower.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_syn_upper.refGene,Number=.,Type=String,Description="oe_syn_upper.refGene annotation provided by ANNOVAR"
##INFO=ID=Function_description.refGene,Number=.,Type=String,Description="Function_description.refGene annotation provided by ANNOVAR"
##INFO=ID=Disease_description.refGene,Number=.,Type=String,Description="Disease_description.refGene annotation provided by ANNOVAR"
##INFO=ID=Tissue_specificity(Uniprot).refGene,Number=.,Type=String,Description="Tissue_specificity(Uniprot).refGene annotation provided by ANNOVAR"
##INFO=ID=CLNALLELEID,Number=.,Type=String,Description="CLNALLELEID annotation provided by ANNOVAR"
##INFO=ID=CLNDN,Number=.,Type=String,Description="CLNDN annotation provided by ANNOVAR"
##INFO=ID=CLNDISDB,Number=.,Type=String,Description="CLNDISDB annotation provided by ANNOVAR"
##INFO=ID=CLNREVSTAT,Number=.,Type=String,Description="CLNREVSTAT annotation provided by ANNOVAR"
##INFO=ID=CLNSIG,Number=.,Type=String,Description="CLNSIG annotation provided by ANNOVAR"
##INFO=ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"
##INFO=ID=SIFT_converted_rankscore,Number=.,Type=String,Description="SIFT_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HDIV_rankscore,Number=.,Type=String,Description="Polyphen2_HDIV_rankscore annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HVAR_rankscore,Number=.,Type=String,Description="Polyphen2_HVAR_rankscore annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"
##INFO=ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"
##INFO=ID=LRT_converted_rankscore,Number=.,Type=String,Description="LRT_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"
##INFO=ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"
##INFO=ID=MutationTaster_converted_rankscore,Number=.,Type=String,Description="MutationTaster_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"
##INFO=ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"
##INFO=ID=MutationAssessor_score_rankscore,Number=.,Type=String,Description="MutationAssessor_score_rankscore annotation provided by ANNOVAR"
##INFO=ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"
##INFO=ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"
##INFO=ID=FATHMM_converted_rankscore,Number=.,Type=String,Description="FATHMM_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"
##INFO=ID=PROVEAN_score,Number=.,Type=String,Description="PROVEAN_score annotation provided by ANNOVAR"
##INFO=ID=PROVEAN_converted_rankscore,Number=.,Type=String,Description="PROVEAN_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=PROVEAN_pred,Number=.,Type=String,Description="PROVEAN_pred annotation provided by ANNOVAR"
##INFO=ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"
##INFO=ID=VEST3_rankscore,Number=.,Type=String,Description="VEST3_rankscore annotation provided by ANNOVAR"
##INFO=ID=MetaSVM_score,Number=.,Type=String,Description="MetaSVM_score annotation provided by ANNOVAR"
##INFO=ID=MetaSVM_rankscore,Number=.,Type=String,Description="MetaSVM_rankscore annotation provided by ANNOVAR"
##INFO=ID=MetaSVM_pred,Number=.,Type=String,Description="MetaSVM_pred annotation provided by ANNOVAR"
##INFO=ID=MetaLR_score,Number=.,Type=String,Description="MetaLR_score annotation provided by ANNOVAR"
##INFO=ID=MetaLR_rankscore,Number=.,Type=String,Description="MetaLR_rankscore annotation provided by ANNOVAR"
##INFO=ID=MetaLR_pred,Number=.,Type=String,Description="MetaLR_pred annotation provided by ANNOVAR"
##INFO=ID=M-CAP_score,Number=.,Type=String,Description="M-CAP_score annotation provided by ANNOVAR"
##INFO=ID=M-CAP_rankscore,Number=.,Type=String,Description="M-CAP_rankscore annotation provided by ANNOVAR"
##INFO=ID=M-CAP_pred,Number=.,Type=String,Description="M-CAP_pred annotation provided by ANNOVAR"
##INFO=ID=REVEL_score,Number=.,Type=String,Description="REVEL_score annotation provided by ANNOVAR"
##INFO=ID=REVEL_rankscore,Number=.,Type=String,Description="REVEL_rankscore annotation provided by ANNOVAR"
##INFO=ID=MutPred_score,Number=.,Type=String,Description="MutPred_score annotation provided by ANNOVAR"
##INFO=ID=MutPred_rankscore,Number=.,Type=String,Description="MutPred_rankscore annotation provided by ANNOVAR"
##INFO=ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"
##INFO=ID=CADD_raw_rankscore,Number=.,Type=String,Description="CADD_raw_rankscore annotation provided by ANNOVAR"
##INFO=ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"
##INFO=ID=DANN_score,Number=.,Type=String,Description="DANN_score annotation provided by ANNOVAR"
##INFO=ID=DANN_rankscore,Number=.,Type=String,Description="DANN_rankscore annotation provided by ANNOVAR"
##INFO=ID=fathmm-MKL_coding_score,Number=.,Type=String,Description="fathmm-MKL_coding_score annotation provided by ANNOVAR"
##INFO=ID=fathmm-MKL_coding_rankscore,Number=.,Type=String,Description="fathmm-MKL_coding_rankscore annotation provided by ANNOVAR"
##INFO=ID=fathmm-MKL_coding_pred,Number=.,Type=String,Description="fathmm-MKL_coding_pred annotation provided by ANNOVAR"
##INFO=ID=Eigen_coding_or_noncoding,Number=.,Type=String,Description="Eigen_coding_or_noncoding annotation provided by ANNOVAR"
##INFO=ID=Eigen-raw,Number=.,Type=String,Description="Eigen-raw annotation provided by ANNOVAR"
##INFO=ID=Eigen-PC-raw,Number=.,Type=String,Description="Eigen-PC-raw annotation provided by ANNOVAR"
##INFO=ID=GenoCanyon_score,Number=.,Type=String,Description="GenoCanyon_score annotation provided by ANNOVAR"
##INFO=ID=GenoCanyon_score_rankscore,Number=.,Type=String,Description="GenoCanyon_score_rankscore annotation provided by ANNOVAR"
##INFO=ID=integrated_fitCons_score,Number=.,Type=String,Description="integrated_fitCons_score annotation provided by ANNOVAR"
##INFO=ID=integrated_fitCons_score_rankscore,Number=.,Type=String,Description="integrated_fitCons_score_rankscore annotation provided by ANNOVAR"
##INFO=ID=integrated_confidence_value,Number=.,Type=String,Description="integrated_confidence_value annotation provided by ANNOVAR"
##INFO=ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"
##INFO=ID=GERP++_RS_rankscore,Number=.,Type=String,Description="GERP++_RS_rankscore annotation provided by ANNOVAR"
##INFO=ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"
##INFO=ID=phyloP100way_vertebrate_rankscore,Number=.,Type=String,Description="phyloP100way_vertebrate_rankscore annotation provided by ANNOVAR"
##INFO=ID=phyloP20way_mammalian,Number=.,Type=String,Description="phyloP20way_mammalian annotation provided by ANNOVAR"
##INFO=ID=phyloP20way_mammalian_rankscore,Number=.,Type=String,Description="phyloP20way_mammalian_rankscore annotation provided by ANNOVAR"
##INFO=ID=phastCons100way_vertebrate,Number=.,Type=String,Description="phastCons100way_vertebrate annotation provided by ANNOVAR"
##INFO=ID=phastCons100way_vertebrate_rankscore,Number=.,Type=String,Description="phastCons100way_vertebrate_rankscore annotation provided by ANNOVAR"
##INFO=ID=phastCons20way_mammalian,Number=.,Type=String,Description="phastCons20way_mammalian annotation provided by ANNOVAR"
##INFO=ID=phastCons20way_mammalian_rankscore,Number=.,Type=String,Description="phastCons20way_mammalian_rankscore annotation provided by ANNOVAR"
##INFO=ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"
##INFO=ID=SiPhy_29way_logOdds_rankscore,Number=.,Type=String,Description="SiPhy_29way_logOdds_rankscore annotation provided by ANNOVAR"
##INFO=ID=Interpro_domain,Number=.,Type=String,Description="Interpro_domain annotation provided by ANNOVAR"
##INFO=ID=GTEx_V6p_gene,Number=.,Type=String,Description="GTEx_V6p_gene annotation provided by ANNOVAR"
##INFO=ID=GTEx_V6p_tissue,Number=.,Type=String,Description="GTEx_V6p_tissue annotation provided by ANNOVAR"
##INFO=ID=dbscSNV_ADA_SCORE,Number=.,Type=String,Description="dbscSNV_ADA_SCORE annotation provided by ANNOVAR"
##INFO=ID=dbscSNV_RF_SCORE,Number=.,Type=String,Description="dbscSNV_RF_SCORE annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_ALL,Number=.,Type=String,Description="gnomAD_exome_ALL annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_AFR,Number=.,Type=String,Description="gnomAD_exome_AFR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_AMR,Number=.,Type=String,Description="gnomAD_exome_AMR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_ASJ,Number=.,Type=String,Description="gnomAD_exome_ASJ annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_EAS,Number=.,Type=String,Description="gnomAD_exome_EAS annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_FIN,Number=.,Type=String,Description="gnomAD_exome_FIN annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_NFE,Number=.,Type=String,Description="gnomAD_exome_NFE annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_OTH,Number=.,Type=String,Description="gnomAD_exome_OTH annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_SAS,Number=.,Type=String,Description="gnomAD_exome_SAS annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_ALL,Number=.,Type=String,Description="gnomAD_genome_ALL annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_AFR,Number=.,Type=String,Description="gnomAD_genome_AFR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_AMR,Number=.,Type=String,Description="gnomAD_genome_AMR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_ASJ,Number=.,Type=String,Description="gnomAD_genome_ASJ annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_EAS,Number=.,Type=String,Description="gnomAD_genome_EAS annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_FIN,Number=.,Type=String,Description="gnomAD_genome_FIN annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_NFE,Number=.,Type=String,Description="gnomAD_genome_NFE annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_OTH,Number=.,Type=String,Description="gnomAD_genome_OTH annotation provided by ANNOVAR"
##INFO=ID=InterVar_automated,Number=.,Type=String,Description="InterVar_automated annotation provided by ANNOVAR"
##INFO=ID=PVS1,Number=.,Type=String,Description="PVS1 annotation provided by ANNOVAR"
##INFO=ID=PS1,Number=.,Type=String,Description="PS1 annotation provided by ANNOVAR"
##INFO=ID=PS2,Number=.,Type=String,Description="PS2 annotation provided by ANNOVAR"
##INFO=ID=PS3,Number=.,Type=String,Description="PS3 annotation provided by ANNOVAR"
##INFO=ID=PS4,Number=.,Type=String,Description="PS4 annotation provided by ANNOVAR"
##INFO=ID=PM1,Number=.,Type=String,Description="PM1 annotation provided by ANNOVAR"
##INFO=ID=PM2,Number=.,Type=String,Description="PM2 annotation provided by ANNOVAR"
##INFO=ID=PM3,Number=.,Type=String,Description="PM3 annotation provided by ANNOVAR"
##INFO=ID=PM4,Number=.,Type=String,Description="PM4 annotation provided by ANNOVAR"
##INFO=ID=PM5,Number=.,Type=String,Description="PM5 annotation provided by ANNOVAR"
##INFO=ID=PM6,Number=.,Type=String,Description="PM6 annotation provided by ANNOVAR"
##INFO=ID=PP1,Number=.,Type=String,Description="PP1 annotation provided by ANNOVAR"
##INFO=ID=PP2,Number=.,Type=String,Description="PP2 annotation provided by ANNOVAR"
##INFO=ID=PP3,Number=.,Type=String,Description="PP3 annotation provided by ANNOVAR"
##INFO=ID=PP4,Number=.,Type=String,Description="PP4 annotation provided by ANNOVAR"
##INFO=ID=PP5,Number=.,Type=String,Description="PP5 annotation provided by ANNOVAR"
##INFO=ID=BA1,Number=.,Type=String,Description="BA1 annotation provided by ANNOVAR"
##INFO=ID=BS1,Number=.,Type=String,Description="BS1 annotation provided by ANNOVAR"
##INFO=ID=BS2,Number=.,Type=String,Description="BS2 annotation provided by ANNOVAR"
##INFO=ID=BS3,Number=.,Type=String,Description="BS3 annotation provided by ANNOVAR"
##INFO=ID=BS4,Number=.,Type=String,Description="BS4 annotation provided by ANNOVAR"
##INFO=ID=BP1,Number=.,Type=String,Description="BP1 annotation provided by ANNOVAR"
##INFO=ID=BP2,Number=.,Type=String,Description="BP2 annotation provided by ANNOVAR"
##INFO=ID=BP3,Number=.,Type=String,Description="BP3 annotation provided by ANNOVAR"
##INFO=ID=BP4,Number=.,Type=String,Description="BP4 annotation provided by ANNOVAR"
##INFO=ID=BP5,Number=.,Type=String,Description="BP5 annotation provided by ANNOVAR"
##INFO=ID=BP6,Number=.,Type=String,Description="BP6 annotation provided by ANNOVAR"
##INFO=ID=BP7,Number=.,Type=String,Description="BP7 annotation provided by ANNOVAR"
##INFO=ID=spliceai_filtered,Number=.,Type=String,Description="spliceai_filtered annotation provided by ANNOVAR"
##INFO=ID=dpsi_max_tissue,Number=.,Type=String,Description="dpsi_max_tissue annotation provided by ANNOVAR"
##INFO=ID=dpsi_zscore,Number=.,Type=String,Description="dpsi_zscore annotation provided by ANNOVAR"
##INFO=ID=PopFreqMax,Number=.,Type=String,Description="PopFreqMax annotation provided by ANNOVAR"
##INFO=ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"
##INFO=ID=MPA_adjusted,Number=.,Type=String,Description="MPA_adjusted : normalize MPA missense score from 0 to 10"
##INFO=ID=MPA_available,Number=.,Type=String,Description="MPA_available : number of missense tools annotation available for this variant"
##INFO=ID=MPA_deleterious,Number=.,Type=String,Description="MPA_deleterious : number of missense tools that annotate this variant pathogenic"
##INFO=ID=MPA_final_score,Number=.,Type=String,Description="MPA_final_score : unique score that take into account curated database, biological assumptions, splicing predictions and the sum of various predictors for missense alterations. Annotations are made for exonic and splicing variants up to +300nt."
##INFO=ID=MPA_impact,Number=.,Type=String,Description="MPA_impact : pathogenic predictions (clinvar_pathogenicity, splice_impact, stop and frameshift_impact)"
##INFO=ID=MPA_ranking,Number=.,Type=String,Description="MPA_ranking : prioritize variants with ranks from 1 to 10"
##FORMAT=ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"
##FORMAT=ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"
##FORMAT=ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"
##FORMAT=ID=GT,Number=1,Type=String,Description="Genotype"
##FORMAT=ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"
##FILTER=ID=LowCoverage,Description="DP 20"
##FILTER=ID=LowMappingQuality,Description="MQ 10.00"
##FILTER=ID=LowQD,Description="QD 1.5"
##FILTER=ID=LowQual,Description="Low quality"
##FILTER=ID=PASS,Description="All filters passed"
##FILTER=ID=R8,Description="POLYX 7"
##FILTER=ID=StrandBias,Description="FS 60.000"
##contig=ID=chr1,length=249250621
##contig=ID=chr2,length=243199373
##contig=ID=chr3,length=198022430
##contig=ID=chr4,length=191154276
##contig=ID=chr5,length=180915260
##contig=ID=chr6,length=171115067
##contig=ID=chr7,length=159138663
##contig=ID=chr8,length=146364022
##contig=ID=chr9,length=141213431
##contig=ID=chr10,length=135534747
##contig=ID=chr11,length=135006516
##contig=ID=chr12,length=133851895
##contig=ID=chr13,length=115169878
##contig=ID=chr14,length=107349540
##contig=ID=chr15,length=102531392
##contig=ID=chr16,length=90354753
##contig=ID=chr17,length=81195210
##contig=ID=chr18,length=78077248
##contig=ID=chr19,length=59128983
##contig=ID=chr20,length=63025520
##contig=ID=chr21,length=48129895
##contig=ID=chr22,length=51304566
##contig=ID=chrX,length=155270560
##contig=ID=chrY,length=59373566
##contig=ID=chrM,length=16571
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B00GMSH B00GMSI B00GMSJ
</div>
<div id="ALL" class="tabcontent">
<table id='table' class="display compact" >
<thead><tr class="head"> <th class="rotate" ><div><span>MPA_ranking </span></div></th>
<th class="rotate" ><div><span>MPA_impact </span></div></th>
<th class="rotate" ><div><span>Phenolyzer </span></div></th>
<th class="rotate" ><div><span>Gene.refGene </span></div></th>
<th class="rotate" ><div><span>Phenotypes.refGene </span></div></th>
<th class="rotate" ><div><span>gnomAD_genome_ALL </span></div></th>
<th class="rotate" ><div><span>gnomAD_exome_ALL </span></div></th>
<th class="rotate" ><div><span>CLNSIG </span></div></th>
<th class="rotate" ><div><span>InterVar_automated </span></div></th>
<th class="rotate" ><div><span>SecondHit-CNV </span></div></th>
<th class="rotate" ><div><span>Func.refGene </span></div></th>
<th class="rotate" ><div><span>Genotype-B00GMSH </span></div></th>
<th class="rotate" ><div><span>Genotype-B00GMSI </span></div></th>
<th class="rotate" ><div><span>Genotype-B00GMSJ </span></div></th>
<th class="rotate" ><div><span>#CHROM </span></div></th>
<th class="rotate" ><div><span>POS </span></div></th>
<th class="rotate" ><div><span>ID </span></div></th>
<th class="rotate" ><div><span>REF </span></div></th>
<th class="rotate" ><div><span>ALT </span></div></th>
<th class="rotate" ><div><span>FILTER </span></div></th>
</tr>
</thead>
<tbody>
<tr class="ALL" >
<td ><div class="tooltip">001<span class="tooltiptext tooltip-bottom">MPA_ranking = 3
MPA_final_score = 10
MPA_impact = splice_impact
MPA_adjusted = 0
MPA_available = 0
MPA_deleterious = 0
--- SPLICE ---
dbscSNV_ADA_SCORE = 0.9954
dbscSNV_RF_SCORE = 0.75
spliceai_filtered DS_AG=0.0000
spliceai_filtered DS_AL=0.0000
spliceai_filtered DS_DG=0.0008
spliceai_filtered DS_DL=0.4060
--- MISSENSE ---
LRT_pred = .
SIFT_pred = .
FATHMM_pred = .
MetaLR_pred = .
MetaSVM_pred = .
PROVEAN_pred = .
Polyphen2_HDIV_pred = .
Polyphen2_HVAR_pred = .
MutationTaster_pred = .
fathmm-MKL_coding_pred = .
</span></div> </td>
<td><div class="tooltip">splice_impact</div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#7FFF00"><div class="tooltip">C1orf159<span class="tooltiptext tooltip-bottom">LOEUF = 1.302
LOEUF_decile = 7.0
oe_lof = 0.69466
oe_lof_lower = 0.394
Missense_upper = 1.016
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">.
Disease_description.refGene:
.
</span></div> </td>
<td ><div class="tooltip">0.0053<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 0.0053
gnomAD_genome_AFR = 0.0014
gnomAD_genome_AMR = 0.0024
gnomAD_genome_ASJ = 0
gnomAD_genome_EAS = 0
gnomAD_genome_FIN = 0.0052
gnomAD_genome_NFE = 0.0084
gnomAD_genome_OTH = 0.0051
</span></div> </td>
<td ><div class="tooltip">0.0047<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 0.0047
gnomAD_exome_AFR = 0.0017
gnomAD_exome_AMR = 0.0017
gnomAD_exome_ASJ = 0.0041
gnomAD_exome_EAS = 0
gnomAD_exome_FIN = 0.0091
gnomAD_exome_NFE = 0.0083
gnomAD_exome_OTH = 0.0049
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td><div class="tooltip">.</div> </td>
<td ><div class="tooltip">splicing;intronic<span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
.
AAChange.refGene:
.
GeneDetail.refGene:
NM_017891:exon2:UTR5
NM_001330306:exon3:UTR5
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 2523.16
Genotype-B00GMSH - 0/1
DP = 96 AD = 52,44 AB = 0.458
Genotype-B00GMSI - 0/0
DP = 110 AD = 109,1 AB = 0.009
Genotype-B00GMSJ - 0/1
DP = 105 AD = 61,44 AB = 0.419
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td><div class="tooltip">chr1</div> </td>
<td><div class="tooltip">1027366</div> </td>
<td><div class="tooltip">rs143221733</div> </td>
<td><div class="tooltip">C</div> </td>
<td><div class="tooltip">T</div> </td>
<td><div class="tooltip">PASS</div> </td>
</tr>
<tr class="ALL" >
<td ><div class="tooltip">002<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 10.0
MPA_impact = missense_impact
MPA_adjusted = 10.0
MPA_available = 10
MPA_deleterious = 10
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered = .
--- MISSENSE ---
LRT_pred = D
SIFT_pred = D
FATHMM_pred = D
MetaLR_pred = D
MetaSVM_pred = D
PROVEAN_pred = D
Polyphen2_HDIV_pred = D
Polyphen2_HVAR_pred = D
MutationTaster_pred = D
fathmm-MKL_coding_pred = D
</span></div> </td>
<td><div class="tooltip">10_missense_impact</div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#00FF00"><div class="tooltip">PLA2G2F<span class="tooltiptext tooltip-bottom">LOEUF = 1.817
LOEUF_decile = 9.0
oe_lof = 1.1229
oe_lof_lower = 0.651
Missense_upper = 1.237
Function Description:
FUNCTION:_May_play_a_role_in_lipid_mediator_production_in_inflammatory_conditions,_by_providing_arachidonic_acid_to_downstream_cyclooxygenases_and_lipoxygenases_(By_similarity)._Phospholipase_A2,_which_catalyzes_the_calcium_dependent_hydrolysis_of_the_2_acyl_groups_in_3_sn_phosphoglycerides_(PubMed:11112443)._Hydrolyzes_phosphatidylethanolamine_more_efficiently_than_phosphatidylcholine,_with_only_a_modest_preference_for_arachidonic_acid_versus_linoelic_acid_at_the_sn_2_position._Comparable_activity_toward_1_palmitoyl_2_oleoyl_phosphatidylserine_vesicles_to_that_toward_1_palmitoyl_2_oleoyl_phosphatidylglycerol_(By_similarity)._Hydrolyzes_phosphatidylglycerol_versus_phosphatidylcholine_with_a_15_fold_preference_(PubMed:11112443)._{ECO:0000250|UniProtKB:Q9QZT4,_ECO:0000269|PubMed:11112443}.
Tissue specificity:
TISSUE_SPECIFICITY:_Expressed_at_high_levels_in_placenta,_testis,_thymus_and_at_lower_levels_in_heart,_kidney,_liver_and_prostate_(PubMed:11112443)._Highly_expressed_in_rheumatoid_arthritic_tissues,_including_synovial_lining_cells_in_the_intima,_capillary_endothelial_cells_and_plasma_cells_(PubMed:11877435)._{ECO:0000269|PubMed:11112443,_ECO:0000269|PubMed:11877435}.
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">.
Disease_description.refGene:
.
</span></div> </td>
<td ><div class="tooltip">3.233e-05<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 3.233e-05
gnomAD_genome_AFR = 0
gnomAD_genome_AMR = 0
gnomAD_genome_ASJ = 0
gnomAD_genome_EAS = 0
gnomAD_genome_FIN = 0
gnomAD_genome_NFE = 0
gnomAD_genome_OTH = 0.0010
</span></div> </td>
<td ><div class="tooltip">4.068e-06<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 4.068e-06
gnomAD_exome_AFR = 0
gnomAD_exome_AMR = 0
gnomAD_exome_ASJ = 0
gnomAD_exome_EAS = 0
gnomAD_exome_FIN = 0
gnomAD_exome_NFE = 8.982e-06
gnomAD_exome_OTH = 0
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">Uncertain_significance<span class="tooltiptext tooltip-bottom">PM1 = 1
Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
PP3 = 1
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.) sfit for conservation, GERP++_RS for evolutionary, splicing impact from dbNSFP
</span></div> </td>
<td><div class="tooltip">.</div> </td>
<td ><div class="tooltip">exonic<span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
nonsynonymous_SNV
AAChange.refGene:
PLA2G2F:NM_022819:exon3:c.G262A:p.G88S
PLA2G2F:NM_022819:exon3:c.262G>A:p.G88S
GeneDetail.refGene:
.
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 2455.16
Genotype-B00GMSH - 0/1
DP = 73 AD = 31,42 AB = 0.575
Genotype-B00GMSI - 0/0
DP = 59 AD = 59,0 AB = 0
Genotype-B00GMSJ - 0/1
DP = 82 AD = 43,39 AB = 0.475
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td><div class="tooltip">chr1</div> </td>
<td><div class="tooltip">20470031</div> </td>
<td><div class="tooltip">.</div> </td>
<td><div class="tooltip">G</div> </td>
<td><div class="tooltip">A</div> </td>
<td><div class="tooltip">PASS</div> </td>
</tr>
<tr class="ALL OMIMREC CANDID_myPatho2" >
<td ><div class="tooltip">003<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 9.0
MPA_impact = missense_impact
MPA_adjusted = 9.0
MPA_available = 10
MPA_deleterious = 9
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered = .
--- MISSENSE ---
LRT_pred = D
SIFT_pred = D
FATHMM_pred = T
MetaLR_pred = D
MetaSVM_pred = D
PROVEAN_pred = D
Polyphen2_HDIV_pred = D
Polyphen2_HVAR_pred = D
MutationTaster_pred = D
fathmm-MKL_coding_pred = D
</span></div> </td>
<td><div class="tooltip">9_missense_impact</div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#FFFF00"><div class="tooltip">H6PD<span class="tooltiptext tooltip-bottom">LOEUF = 0.941
LOEUF_decile = 5.0
oe_lof = 0.6271399999999999
oe_lof_lower = 0.428
Missense_upper = 1.23
Function Description:
FUNCTION:_Bifunctional_enzyme_localized_in_the_lumen_of_the_endoplasmic_reticulum_that_catalyzes_the_first_two_steps_of_the_oxidative_branch_of_the_pentose_phosphate_pathway/shunt,_an_alternative_to_glycolysis_and_a_major_source_of_reducing_power_and_metabolic_intermediates_for_biosynthetic_processes_(By_similarity)._Has_a_hexose_6_phosphate_dehydrogenase_activity,_with_broad_substrate_specificity_compared_to_glucose_6_phosphate_1_dehydrogenase/G6PD,_and_catalyzes_the_first_step_of_the_pentose_phosphate_pathway_(PubMed:12858176,_PubMed:18628520,_PubMed:23132696)._In_addition,_acts_as_a_6_phosphogluconolactonase_and_catalyzes_the_second_step_of_the_pentose_phosphate_pathway_(By_similarity)._May_have_a_dehydrogenase_activity_for_alternative_substrates_including_glucosamine_6_phosphate_and_glucose_6_sulfate_(By_similarity)._The_main_function_of_this_enzyme_is_to_provide_reducing_equivalents_such_as_NADPH_to_maintain_the_adequate_levels_of_reductive_cofactors_in_the_oxidizing_environment_of_the_endoplasmic_reticulum_(PubMed:12858176,_PubMed:18628520,_PubMed:23132696)._By_producing_NADPH_that_is_needed_by_reductases_of_the_lumen_of_the_endoplasmic_reticulum_like_corticosteroid_11_beta_dehydrogenase_isozyme_1/HSD11B1,_indirectly_regulates_their_activity_(PubMed:18628520)._{ECO:0000250|UniProtKB:Q8CFX1,_ECO:0000269|PubMed:12858176,_ECO:0000269|PubMed:18628520,_ECO:0000269|PubMed:23132696}.
Tissue specificity:
TISSUE_SPECIFICITY:_Present_in_most_tissues_examined,_strongest_in_liver._{ECO:0000269|PubMed:10349511}.
</span></div> </td>
<td ><div class="tooltip">Cortisone_reductase_deficiency_1,_604931__3_,_Autosomal_recessive<span class="tooltiptext tooltip-bottom">Cortisone_reductase_deficiency_1,_604931__3_,_Autosomal_recessive
Disease_description.refGene:
DISEASE:_Cortisone_reductase_deficiency_1_(CORTRD1)_[MIM:604931]:_An_autosomal_recessive_error_of_cortisone_metabolism_characterized_by_a_failure_to_regenerate_cortisol_from_cortisone,_resulting_in_increased_cortisol_clearance,_activation_of_the_hypothalamic_pituitary_axis_and_ACTH_mediated_adrenal_androgen_excess._Clinical_features_include_hyperandrogenism_resulting_in_hirsutism,_oligo_amenorrhea,_and_infertility_in_females_and_premature_pseudopuberty_in_males._{ECO:0000269|PubMed:12858176,_ECO:0000269|PubMed:17974005,_ECO:0000269|PubMed:18628520,_ECO:0000269|PubMed:23132696}._Note=The_disease_is_caused_by_mutations_affecting_the_gene_represented_in_this_entry.
</span></div> </td>
<td ><div class="tooltip">3.233e-05<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 3.233e-05
gnomAD_genome_AFR = 0.0001
gnomAD_genome_AMR = 0
gnomAD_genome_ASJ = 0
gnomAD_genome_EAS = 0
gnomAD_genome_FIN = 0
gnomAD_genome_NFE = 0
gnomAD_genome_OTH = 0
</span></div> </td>
<td ><div class="tooltip">8.577e-06<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 8.577e-06
gnomAD_exome_AFR = 7.179e-05
gnomAD_exome_AMR = 0
gnomAD_exome_ASJ = 0
gnomAD_exome_EAS = 0
gnomAD_exome_FIN = 0
gnomAD_exome_NFE = 9.54e-06
gnomAD_exome_OTH = 0
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">Uncertain_significance<span class="tooltiptext tooltip-bottom">PM2 = 1
Absent from controls (or at extremely low frequency if recessive) (Table 6) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
PM1 = 1
Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
PP3 = 1
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.) sfit for conservation, GERP++_RS for evolutionary, splicing impact from dbNSFP
</span></div> </td>
<td><div class="tooltip">.</div> </td>
<td ><div class="tooltip">exonic<span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
nonsynonymous_SNV
AAChange.refGene:
H6PD:NM_001282587:exon5:c.C1802T:p.S601L
H6PD:NM_004285:exon5:c.C1769T:p.S590L
H6PD:NM_001282587:exon5:c.1802C>T:p.S601L
H6PD:NM_004285:exon5:c.1769C>T:p.S590L
GeneDetail.refGene:
.
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 3859.16
Genotype-B00GMSH - 0/1
DP = 100 AD = 48,52 AB = 0.52
Genotype-B00GMSI - 0/1
DP = 143 AD = 71,72 AB = 0.503
Genotype-B00GMSJ - 0/0
DP = 137 AD = 137,0 AB = 0
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td><div class="tooltip">chr1</div> </td>
<td><div class="tooltip">9324321</div> </td>
<td><div class="tooltip">.</div> </td>
<td><div class="tooltip">C</div> </td>
<td><div class="tooltip">T</div> </td>
<td><div class="tooltip">PASS</div> </td>
</tr>
<tr class="ALL CANDID_myPatho1" >
<td ><div class="tooltip">004<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 7.0
MPA_impact = missense_impact
MPA_adjusted = 7.0
MPA_available = 10
MPA_deleterious = 7
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered = .
--- MISSENSE ---
LRT_pred = D
SIFT_pred = D
FATHMM_pred = T
MetaLR_pred = T
MetaSVM_pred = T
PROVEAN_pred = D
Polyphen2_HDIV_pred = D
Polyphen2_HVAR_pred = D
MutationTaster_pred = D
fathmm-MKL_coding_pred = D
</span></div> </td>
<td><div class="tooltip">7_missense_impact</div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#FF9900"><div class="tooltip">EPHA8<span class="tooltiptext tooltip-bottom">LOEUF = 0.712
LOEUF_decile = 3.0
oe_lof = 0.506
oe_lof_lower = 0.365
Missense_upper = 0.987
Function Description:
FUNCTION:_Receptor_tyrosine_kinase_which_binds_promiscuously_GPI_anchored_ephrin_A_family_ligands_residing_on_adjacent_cells,_leading_to_contact_dependent_bidirectional_signaling_into_neighboring_cells._The_signaling_pathway_downstream_of_the_receptor_is_referred_to_as_forward_signaling_while_the_signaling_pathway_downstream_of_the_ephrin_ligand_is_referred_to_as_reverse_signaling._The_GPI_anchored_ephrin_A_EFNA2,_EFNA3,_and_EFNA5_are_able_to_activate_EPHA8_through_phosphorylation._With_EFNA5_may_regulate_integrin_mediated_cell_adhesion_and_migration_on_fibronectin_substrate_but_also_neurite_outgrowth._During_development_of_the_nervous_system_plays_also_a_role_in_axon_guidance._Downstream_effectors_of_the_EPHA8_signaling_pathway_include_FYN_which_promotes_cell_adhesion_upon_activation_by_EPHA8_and_the_MAP_kinases_in_the_stimulation_of_neurite_outgrowth_(By_similarity)._{ECO:0000250}.;FUNCTION:_Receptor_tyrosine_kinase_which_binds_promiscuously_GPI_anchored_ephrin_A_family_ligands_residing_on_adjacent_cells,_leading_to_contact_dependent_bidirectional_signaling_into_neighboring_cells._The_signaling_pathway_downstream_of_the_receptor_is_referred_to_as_forward_signaling_while_the_signaling_pathway_downstream_of_the_ephrin_ligand_is_referred_to_as_reverse_signaling._The_GPI_anchored_ephrin_A_EFNA2,_EFNA3,_and_EFNA5_are_able_to_activate_EPHA8_through_phosphorylation._With_EFNA5_may_regulate_integrin_mediated_cell_adhesion_and_migration_on_fibronectin_substrate_but_also_neurite_outgrowth._During_development_of_the_nervous_system_plays_also_a_role_in_axon_guidance._Downstream_effectors_of_the_EPHA8_signaling_pathway_include_FYN_which_promotes_cell_adhesion_upon_activation_by_EPHA8_and_the_MAP_kinases_in_the_stimulation_of_neurite_outgrowth_(By_similarity)._{ECO:0000250}.
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">.
Disease_description.refGene:
.
</span></div> </td>
<td ><div class="tooltip">0<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 0
gnomAD_genome_AFR = .
gnomAD_genome_AMR = .
gnomAD_genome_ASJ = .
gnomAD_genome_EAS = .
gnomAD_genome_FIN = .
gnomAD_genome_NFE = .
gnomAD_genome_OTH = .
</span></div> </td>
<td ><div class="tooltip">0<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 0
gnomAD_exome_AFR = .
gnomAD_exome_AMR = .
gnomAD_exome_ASJ = .
gnomAD_exome_EAS = .
gnomAD_exome_FIN = .
gnomAD_exome_NFE = .
gnomAD_exome_OTH = .
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">Uncertain_significance<span class="tooltiptext tooltip-bottom">PM2 = 1
Absent from controls (or at extremely low frequency if recessive) (Table 6) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
PM1 = 1
Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
</span></div> </td>
<td><div class="tooltip">.</div> </td>
<td ><div class="tooltip">exonic<span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
nonsynonymous_SNV
AAChange.refGene:
EPHA8:NM_020526:exon10:c.A1892G:p.E631G
EPHA8:NM_020526:exon10:c.1892A>G:p.E631G
GeneDetail.refGene:
.
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 3067.16
Genotype-B00GMSH - 0/1
DP = 105 AD = 53,52 AB = 0.495
Genotype-B00GMSI - 0/0
DP = 138 AD = 138,0 AB = 0
Genotype-B00GMSJ - 0/1
DP = 148 AD = 81,67 AB = 0.452
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td><div class="tooltip">chr1</div> </td>
<td><div class="tooltip">22923931</div> </td>
<td><div class="tooltip">.</div> </td>
<td><div class="tooltip">A</div> </td>
<td><div class="tooltip">G</div> </td>
<td><div class="tooltip">PASS</div> </td>
</tr>
<tr class="ALL" >
<td ><div class="tooltip">005<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 7.0
MPA_impact = missense_impact,splice_impact
MPA_adjusted = 7.0
MPA_available = 10
MPA_deleterious = 7
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered DS_AG=0.3887
spliceai_filtered DS_AL=0.0000
spliceai_filtered DS_DG=0.0000
spliceai_filtered DS_DL=0.0000
--- MISSENSE ---
LRT_pred = D
SIFT_pred = D
FATHMM_pred = T
MetaLR_pred = T
MetaSVM_pred = T
PROVEAN_pred = D
Polyphen2_HDIV_pred = D
Polyphen2_HVAR_pred = D
MutationTaster_pred = D
fathmm-MKL_coding_pred = D