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Table 4 Confirmation of genotypes from 26 ambiguous variations calls

From: Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection

  European African Asian   Huvariome
Chromosome Position Reference base Amino acid change Gene NA12156 NA12878 NA18507 NA18517 NA19129 NA19240 NA18555 NA18956 Change European African Asian
2 227829345 G ASP,TYR COL4A3 K G G G G G G G K G:T   G:T
6 71029714 T GLU,GLY COL9A1 Y T T T T T T T Y T:T T:T T:T
14 70059717 T TYR,CYS ADAM20 Y T T T T T T T Y T:T T:T T:T
16 28511156 T ASN,THR SULT1A2 K T T T T T T T K T:G T:G T:G
9 100837151 C PRO,LEU COL15A1 C Y C C C C C C Y C:C   
14 69994396 T TYR,HIS ADAM21 T Y T T T T T T Y T:T T:T T:T
16 28514697 G PRO,LEU SULT1A2 G R G G G G G G R G:A G:A  
2 227632472 G PRO,LEU COL4A4 G G R G G G G G R   G:A  
2 237945216 G ARG,TRP COL6A3 G G R G G G G G R   G:A  
6 32286548 C GLY,ARG NOTCH4 C C Y C C C C C Y   C:T  
10 123233227 C ARG,GLN FGFR2 C C Y C C C C C Y C:C C:C C:C
15 72802259 A ILE,THR CYP1A1 A A R A A A A A R   A:G  
15 82491107 T MET,THR ADAMTSL3 T T Y T T T T T Y   T:C  
19 46210061 T ILE,THR CYP2B6 T T Y T T T T T Y T:T T:T T:T
4 73407648 C GLY,ARG ADAMTS3 C C C Y C C C C Y   C:T  
6 46728211 C ARG,PRO CYP39A1 C C C S C C C C S C:G C:G  
7 99283117 G ARG,GLN CYP3A43 G G G R G G G G R   G:A  
10 96474119 G VAL,LEU CYP2C18 G G G K G G G G K   G:T  
10 96698964 A HIS,ARG CYP2C9 A A A R A A A A R   A:G  
15 76845583 G PRO,LEU ADAMTS7 G G G R G G G G R   G:A  
1 120269806 C GLY,ARG NOTCH2 C C C C C Y C C Y C:C C:C C:C
8 24420887 C PRO,LEU ADAM7 C C C C C Y C C Y C:C C:C C:C
17 38961570 G PRO,LEU ETV4 G G G G G G R G R    G:A
21 46365928 C PRO,THR COL6A2 C C C C C C M C M    C:A
2 189622367 G PRO,LEU COL5A2 G G G G G G G R R    G:A
5 129100767 C THR,ILE ADAMTS19 C C C C C C C T T   C:T  
  1. Results from Huvariome analysis of 26 selected coding SNVs to disambiguate genetic variation determined by Ng et al. 2009 [24]. The first 7 columns display the normal variations and their proposed functional impact, determined by Ng et al. 2009. The base changes are presented as the IUPAC codes per sample (e.g. NA12156), which are grouped by populations, CEU (NA12156, NA12878), YRI (NA18507, NA18517, NA19129, NA19240), Asian (NA18555, NA18956), with the impacted bases denoted with bold letters, and in the column titled “change”. The last three columns contain the genotypes called for the three populations present in Huvariome Core and the Diversity Panel (European, African, and Asian). The Huvariome genotypes highlighted as bold demonstrate that Huvariome calls homozygous reference while the genotypes are heterozygous reference.