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

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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