Table 2 (a) SNPs in different annotation categories for overall Bangladeshi native chicken populations. (b) Sumary statistics of SNPs in Bangladeshi improved and unimproved native chicken populations.

Exonic Variants

Synonymous variant

232,772

1.050

Missense variant

140,947

0.636

Stop-gained variant

2,040

0.009

Stop-lost variant

246

0.001

Start-lost variant

1,050

0.005

Stop-retained variant

171

0.001

Coding sequence variant

1

0.000

Splicing Variants

Splice acceptor variant

1,925

0.009

Splice donor variant

2,733

0.012

Splice donor 5^th base variant

3,120

0.014

Splice region variant

46,812

0.211

Splice donor region variant

9,705

0.044

Splice polypyrimidine tract variant

39,445

0.178

Intronic Variants

Intron variant

15,111,660

68.181

Intergenic Variants

Intergenic variant

2,964,795

13.377

Regulatory Variants

Upstream gene variant

1,342,998

6.059

Downstream gene variant

835,260

3.769

UTR variants

5 prime UTR variant

144,292

0.651

3 prime UTR variant

473,793

2.138

Other variants

Mature miRNA variant

230

0.001

Non-coding transcript exon variant

809,920

3.654

22,163,915

100.00

Chicken populations

Total SNPs

Novel SNPs

Novel SNPs %

Ts/Tv Ratio

Singletons (%)

CD_Imp

14,585,310

1,646,054

11.29

2.482

16.57

CD_Unimp

17,142,624

2,677,720

15.62

2.475

23.61

HL_Imp

13,792,070

1,493,434

10.83

2.485

14.8

HL_Unimp

15,873,233

2,257,509

14.22

2.479

20.84

NN_Imp

11,889,880

992,111

8.34

2.492

12.52

NN_Unimp

17,041,300

2,632,800

15.45

2.475

23.11

Overall Bangladeshi native chicken population

22,163,915

5,553,897

25.1

2.453

13.64