69 Genomes Data Interpretation

Question

[Pappu]

I am trying to analyze CompletePublicGenomes69genomesall_testvariants.tsv file. But I could not understand the meaning of keywords: NN , 00, 1N, 01,11,10,N1 etc. Please let me know the meaning of them. Thank you.

variantId       chromosome      begin   end     varType reference       alleleSeq       xRef    HG00731-200-37-ASM      
HG00732-200-37-ASM      HG00733-200-37-ASM      NA06985-200-37-ASM      NA06994-200-37-ASM      NA07357-200-37-ASM      
NA10851-200-37-ASM      NA12004-200-37-ASM      NA12877-200-37-ASM      NA12878-200-37-ASM      NA12879-200-37-ASM           NA12880-200-37-ASM      NA12881-200-37-ASM      NA12882-200-37-ASM      NA12883-200-37-ASM      NA12884-200-37-ASM          NA12885-L2-200-37-ASM   NA12886-L2-200-37-ASM   NA12887-L2-200-37-ASM   NA12888-200-37-ASM      NA12889-L2-200-37-    ASM   NA12890-200-37-ASM      NA12891-200-37-ASM      NA12892-L2-200-37-ASM   NA12893-200-37-ASM      NA18501-200-37-    ASM      NA18502-200-37-ASM      NA18504-200-37-ASM      NA18505-200-37-ASM      NA18508-200-37-ASM      NA18517-200-37-    ASM      NA18526-200-37-ASM      NA18537-200-37-ASM      NA18555-200-37-ASM      NA18558-200-37-ASM      NA18940-200-37-    ASM      NA18942-200-37-ASM      NA18947-200-37-ASM      NA18956-200-37-ASM      NA19017-200-37-ASM      NA19020-200-37-    ASM      NA19025-200-37-ASM      NA19026-200-37-ASM      NA19129-200-37-ASM      NA19238-L2-200-37-ASM   NA19239-L2-    200-37-ASM   NA19240-L2-200-37-ASM   NA19648-200-37-ASM      NA19649-200-37-ASM      NA19669-200-37-ASM      NA19670-    200-37-ASM      NA19700-200-37-ASM      NA19701-200-37-ASM      NA19703-200-37-ASM      NA19704-200-37-ASM      NA19735-    200-37-ASM      NA19834-200-37-ASM      NA20502-200-37-ASM      NA20509-200-37-ASM      NA20510-200-37-ASM      NA20511-    200-37-ASM      NA20845-200-37-ASM      NA20846-200-37-ASM      NA20847-200-37-ASM      NA20850-200-37-ASM      NA21732-200-37-ASM      NA21733-200-37-ASM      NA21737-200-37-ASM      NA21767-200-37-ASM

1       chr1    11013   11014   snp     G       A       dbsnp.125:    NN      NN      NN      NN      NN      NN      NN
  NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      1N
  NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN
  NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN
  NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN

2       chr1    11021   11022   snp     G       A       dbsnp.125:;dbsnp.129:       NN      NN      NN      NN
  NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      00      NN      NN      NN
  NN      NN      1N      00      00      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN
  NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN
  NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN      NN
  NN

Answer 1

[JC]

Those fields refer to the individual genotypes: N=NoCall, 0=ReferenceAllele, 1=AlternativeAllele, therefore NN=NoCalls in both alleles, 00=reference homozygous, 1N=AlternativeAllele+NoCall, 01=heterozygous (Reference+Alternative), 10=heterozygous (Alternative+Reference), 11=AlternativeAllele homozygous, ...

You can learn more about Complete Genomic data formats in their website.