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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