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Table 2 Sanger Sequence Calls vs. Maq

From: Exome-wide DNA capture and next generation sequencing in domestic and wild species

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
  1. 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.