- Export Date: 2019-Feb-05 06:40:19
- Analysis Name : CCF-CAYA-012519
Ingenuity Variant Analysis version 5.4.20190121 Content versions:
CADD (v1.3),
Allele Frequency Community (2018-09-06),
EVS (ESP6500SI-V2),
Refseq Gene Model (2018-07-10),
JASPAR (2013-11),
Ingenuity Knowledge Base Snapshot Timestamp (2019-01-06 00:23:50.0),
Vista Enhancer (2012-07),
Clinical Trials (Stepford 190106.000),
PolyPhen-2 (v2.2.2),
1000 Genome Frequency (phase3v5b),
ExAC (0.3.1),
iva (Oct 4 11:04 iva-1.0.736.jar),
PhyloP (2009-11),
DbSNP (151),
TargetScan (6.2),
GENCODE (Release 28),
CentoMD (5.0),
Ingenuity Knowledge Base (Stepford 190106.000),
OMIM (May 26, 2017),
gnomAD (2.0.1),
BSIFT (2016-02-23),
TCGA (2013-09-05),
Clinvar (2018-08-01),
DGV (2016-05-15),
COSMIC (v86),
HGMD (2018.3),
SIFT4G (2016-02-23)
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Starting with 55,346 variants spanning 18,630 genes, variants were:
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kept with call quality at least 20.0 in cases or at least 20.0 in controls AND pass upstream pipeline filtering AND with read depth at least 20.0 in cases or at least 20.0 in controls AND with allele fraction at least 20.0 in cases or at least 20.0 in controls with genotype quality at least 30.0 in cases or at least 30.0 in controls AND outside top 5.0% most exonically variable 100base windows in healthy public genomes (1000 genomes)
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excluded that are observed with an allele frequency greater than or equal to 1.0% of the genomes in the 1000 genomes project OR greater than or equal to 1.0% of the NHLBI ESP exomes (All) OR greater than or equal to 1.0% of the ExAC Frequency OR greater than or equal to 1.0% of the gnomAD Maximum Frequency OR Filter variants unless established Pathogenic common variant
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kept (up to 20 bases into intron) that are experimentally observed to be associated with a phenotype: Pathogenic, Possibly Pathogenic
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excluded that are on chromosome MT
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kept which occur in at least 1 of the case samples at the variant level in the Case samples AND not which occur in at least 1 of the control samples at the variant level in the Control Samples
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kept (up to 20 bases into intron) that are experimentally observed to be associated with a phenotype: Pathogenic, Possibly Pathogenic OR Disease-associated according to HGMD OR predicted to disrupt splicing by MaxEntScan
BarCode Name Description Subject Status
CCF13084-01-001 CCF13084-01-001 CCF13084-01-001 CASE
CCF13090-01-001 CCF13090-01-001 CCF13090-01-001 CASE
CCF13037-01-001 CCF13037-01-001 CCF13037-01-001 CASE
CCF13105-01-001 CCF13105-01-001 CCF13105-01-001 CASE
CCF10699-01-001_R1 CCF10699-01-001_R1 CCF10699-01-001_R1 CASE
CCF10723_TAAGGCG-TAAGGA_R1.fastq CCF10723_TAAGGCG-TAAGGA_R1.fastq CCF10723_TAAGGCG-TAAGGA_R1.fastq CASE
CCF10769_CGTACTA-TAAGGA_R1.fastq CCF10769_CGTACTA-TAAGGA_R1.fastq CCF10769_CGTACTA-TAAGGA_R1.fastq CASE
CCF10770_AGGCAGA-TAAGGA_R1.fastq CCF10770_AGGCAGA-TAAGGA_R1.fastq CCF10770_AGGCAGA-TAAGGA_R1.fastq CASE
CCF10771_TCCTGAG-TAAGGA_R1.fastq CCF10771_TCCTGAG-TAAGGA_R1.fastq CCF10771_TCCTGAG-TAAGGA_R1.fastq CASE
CCF10781_GGACTCC-TAAGGA_R1.fastq CCF10781_GGACTCC-TAAGGA_R1.fastq CCF10781_GGACTCC-TAAGGA_R1.fastq CASE
CCF10782_TAGGCAT-TAAGGA_R1.fastq CCF10782_TAGGCAT-TAAGGA_R1.fastq CCF10782_TAGGCAT-TAAGGA_R1.fastq CASE
CCF10783_CTCTCTA-TAAGGA_R1.fastq CCF10783_CTCTCTA-TAAGGA_R1.fastq CCF10783_CTCTCTA-TAAGGA_R1.fastq CASE
CCF10839_GCTACGC-TAAGGA_R1.fastq CCF10839_GCTACGC-TAAGGA_R1.fastq CCF10839_GCTACGC-TAAGGA_R1.fastq CASE
CCF10903_AAGAGGC-TAAGGA_R1.fastq CCF10903_AAGAGGC-TAAGGA_R1.fastq CCF10903_AAGAGGC-TAAGGA_R1.fastq CASE
CCF11008_GTAGAGG-TAAGGA_R1.fastq CCF11008_GTAGAGG-TAAGGA_R1.fastq CCF11008_GTAGAGG-TAAGGA_R1.fastq CASE
CCF11143_TAAGGCG-CTGCAT_R1.fastq CCF11143_TAAGGCG-CTGCAT_R1.fastq CCF11143_TAAGGCG-CTGCAT_R1.fastq CASE
CCF11170_CGTACTA-CTGCAT_R1.fastq CCF11170_CGTACTA-CTGCAT_R1.fastq CCF11170_CGTACTA-CTGCAT_R1.fastq CASE
CCF11171_AGGCAGA-CTGCAT_R1.fastq CCF11171_AGGCAGA-CTGCAT_R1.fastq CCF11171_AGGCAGA-CTGCAT_R1.fastq CASE
CCF11485_GGACTCC-CTGCAT_R1.fastq CCF11485_GGACTCC-CTGCAT_R1.fastq CCF11485_GGACTCC-CTGCAT_R1.fastq CASE
CCF11521-01-001_R1 CCF11521-01-001_R1 CCF11521-01-001_R1 CASE
CCF11769 CCF11769 CCF11769 CASE
CCF11777-01-001_R1 CCF11777-01-001_R1 CCF11777-01-001_R1 CASE
CCF11805-01-001_R1 CCF11805-01-001_R1 CCF11805-01-001_R1 CASE
CCF11813-01-001_R1 CCF11813-01-001_R1 CCF11813-01-001_R1 CASE
CCF11814 CCF11814 CCF11814 CASE
CCF11829-01-001_R1 CCF11829-01-001_R1 CCF11829-01-001_R1 CASE
CCF11834 CCF11834 CCF11834 CASE
CCF11835 CCF11835 CCF11835 CASE
CCF11848 CCF11848 CCF11848 CASE
CCF11884 CCF11884 CCF11884 CASE
CCF11930 CCF11930 CCF11930 CASE
CCF11946 CCF11946 CCF11946 CASE
CCF11950 CCF11950 CCF11950 CASE
CCF11987 CCF11987 CCF11987 CASE
CCF11993 CCF11993 CCF11993 CASE
CCF12007-01-001_R1 CCF12007-01-001_R1 CCF12007-01-001_R1 CASE
CCF12020 CCF12020 CCF12020 CASE
CCF12039 CCF12039 CCF12039 CASE
CCF12040-01-001_R1 CCF12040-01-001_R1 CCF12040-01-001_R1 CASE
CCF12064-01-001_R1 CCF12064-01-001_R1 CCF12064-01-001_R1 CASE
CCF12081 CCF12081 CCF12081 CASE
CCF12082-01-001_R1 CCF12082-01-001_R1 CCF12082-01-001_R1 CASE
CCF12094 CCF12094 CCF12094 CASE
CCF12130 CCF12130 CCF12130 CASE
CCF12189 CCF12189 CCF12189 CASE
CCF12237-01-001_S1_R1 CCF12237-01-001_S1_R1 CCF12237-01-001_S1_R1 CASE
CCF12311-01-001_S2_R1 CCF12311-01-001_S2_R1 CCF12311-01-001_S2_R1 CASE
CCF12327-01-001_S3_R1 CCF12327-01-001_S3_R1 CCF12327-01-001_S3_R1 CASE
CCF11804-01-001 CCF11804-01-001 CCF11804-01-001 CASE
CCF13072-01-001 CCF13072-01-001 CCF13072-01-001 CASE
5476M 5476M 5476M CONTROL
6472M 6472M 6472M CONTROL
4506M 4506M 4506M CONTROL
4469M 4469M 4469M CONTROL
4367M 4367M 4367M CONTROL
4310M 4310M 4310M CONTROL
4214M 4214M 4214M CONTROL
4206M 4206M 4206M CONTROL
3298M 3298M 3298M CONTROL
3048M 3048M 3048M CONTROL
3083M 3083M 3083M CONTROL
1478M 1478M 1478M CONTROL
2994M 2994M 2994M CONTROL