Table 2

Sanger Sequence Calls vs. Maq

sample

chrom

sanger start

sanger stop

position

reference

sanger

maq

gene

bison

chr6

88531917

88532399

88532280

A

G

G

CSN3

bison

chr6

88531917

88532399

88532296

T

C

C

CSN3

zebu

chr6

88531917

88532399

88532296

T

Y

Y

CSN3

zebu

chr6

88531917

88532399

88532332

C

M

M

CSN3

zebu

chr6

88531917

88532399

88532339

A

R

R

CSN3

zebu

chr6

88531917

88532399

88532393

G

R

R

CSN3

taurine

chr6

88531917

88532399

88532293

C

C

Y

CSN3

taurine

chr6

88531917

88532399

88532296

T

T

C

CSN3

taurine

chr6

88531917

88532399

88532393

G

G

A

CSN3

bison

chr4

95689756

95690201

95690049

T

C

C

LEPTIN

zebu

chr4

95689756

95690201

95690049

T

C

C

LEPTIN

taurine

chr4

95689756

95690201

95690049

T

C

C

LEPTIN

bison

chr10

3941758

3942115

3941786

T

C

C

TICAM2

bison

chr10

3941758

3942115

3941805

A

G

G

TICAM2

bison

chr10

3941758

3942115

3941921

A

G

G

TICAM2

bison

chr10

3941758

3942115

3941934

G

A

A

TICAM2

bison

chr10

3941758

3942115

3941946

A

G

G

TICAM2

zebu

chr10

3941758

3942115

3941921

A

G

G

TICAM2

zebu

chr10

3941758

3942115

3941946

A

R

R

TICAM2

zebu

chr10

3941758

3942115

3941963

C

Y

Y

TICAM2

taurine

chr10

3941758

3942115

3941921

A

R

R

TICAM2

bison

chr17

4284137

4284804

4284160

T

A

A

TLR2

bison

chr17

4284137

4284804

4284210

A

G

G

TLR2

bison

chr17

4284137

4284804

4284358

C

Y

Y

TLR2

bison

chr17

4284137

4284804

4284655

T

C

C

TLR2

bison

chr17

4284137

4284804

4284747

C

T

T

TLR2

zebu

chr17

4284137

4284804

4284160

T

W

W

TLR2

zebu

chr17

4284137

4284804

4284210

A

G

G

TLR2

zebu

chr17

4284137

4284804

4284652

G

K

K

TLR2

zebu

chr17

4284137

4284804

4284655

T

Y

Y

TLR2

taurine

chr17

4284137

4284804

4284210

A

R

R

TLR2

taurine

chr17

4284137

4284804

4284639

G

G

R

TLR2

taurine

chr17

4284137

4284804

4284652

G

K

K

TLR2

taurine

chr17

4284137

4284804

4284655

T

T

Y

TLR2

bison

chr8

112427182

112427427

112427204

C

T

T

TLR4

bison

chr8

112427182

112427427

112427213

C

T

T

TLR4

bison

chr8

112427182

112427427

112427326

A

C

C

TLR4

bison

chr8

112431812

112432152

112431927

G

A

A

TLR4

bison

chr8

112434757

112435132

112435011

A

C

C

TLR4

bison

chr8

112434757

112435132

112435120

C

A

A

TLR4


Variant calls in several Sanger sequenced fragments in and near exons in the genes indicated, compared with Maq consensus bases. All variant calls in the Sanger sequenced regions for the bison and zebu are in agreement with the Maq consensus bases. For the taurine five positions (rows in bold) are called as variant by the Maq consensus but not by the Sanger sequenced fragments.

Cosart et al. BMC Genomics 2011 12:347   doi:10.1186/1471-2164-12-347

Open Data