SIFT analysis input and output file
Sometimes when I do a sift analysis, I noticed that the input and output alleles are different. I don't understand why and what does it means ? could you explain it to me ? For example, here you can see that the input allele is G/A for chr2 (first line) and the output is G/T * input file: chr2 230341630 + G/A chr2 43881517 + A/T chr10 115912482 - G/T chr10 115900918 - C/T * output file: #Chrom Position Strand Allele Codons Transcript ID Protein ID Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA EXON CDS rs1803846:A Unknown Not scored NA NA NA chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A Regards. Charlotte Gueydan -- *Charlotte Gueydan *, PhD. INSERM/Université Pierre et Marie Curie Hôpital Tenon - bâtiment de recherche 4, rue de la Chine 75020 Paris cedex 20 tel : 01 56 01 83 75
Hello Charlotte, Would you be able to share a history containing your data run? Options -> Share or Publish. Please email me the link and I will take a look. You can mail to me directly. Thank you, Jen Galaxy team On 6/28/11 8:08 AM, Charlotte Gueydan wrote:
Sometimes when I do a sift analysis, I noticed that the input and output alleles are different. I don't understand why and what does it means ? could you explain it to me ? For example, here you can see that the input allele is G/A for chr2 (first line) and the output is G/T
*
input file:
chr2 230341630 + G/A chr2 43881517 + A/T chr10 115912482 - G/T chr10 115900918 - C/T
*
output file:
#Chrom Position Strand Allele Codons Transcript ID Protein ID Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA EXON CDS rs1803846:A Unknown Not scored NA NA NA chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A
Regards.
Charlotte Gueydan -- *Charlotte Gueydan *, PhD. INSERM/Université Pierre et Marie Curie Hôpital Tenon - bâtiment de recherche 4, rue de la Chine 75020 Paris cedex 20 tel : 01 56 01 83 75
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participants (2)
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Charlotte Gueydan -
Jennifer Jackson