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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.