Table 1 SNP id, chromosome and contig locations including Linkage Disequilibrium between SNP pairs on the same chromosome. D' was calculated by EM algorithm between pairs of SNPs in adjacent order

027.sp6

[Genbank: NW_001493890]

3818758

ss_182258874

Non coding intronic

027.sp6 - 421_10 D' = 0.18

421_10

[Genbank: NW_001493804]

583808

ss_182258864

Non coding intronic

MBS029-1

[Genbank: NW_001494698]

3047667

rs17871918

Non Coding

MBS029-1 - MBS042-1 D' = 0.02

MBS042-1

[Genbank: NW_001494591]

108095

rs41257512

Non coding intronic

018.sp6

[Genbank: NW_001494745]

2606666

ss_182258872

Non coding intronic

018.SP6 - 486_67 D' = 0.41

486_67

[Genbank: NW_001494789]

1283668

ss_182258886

Non Coding

417_16

[Genbank: NW_001494939]

1975758

ss_182258885

Non Coding

417_16 - MBS048-1 D' = 0.12

MBS048-1

[Genbank: NW_001494921]

1019822

rs17871345

Non coding intronic

431_A2

[Genbank: NW_001495040]

1991472

ss_182258884

Non Coding

Exclude SNP MBS030-1

MBS007-1 - 431_A2 D' = 0.09

MBS007-1

[Genbank: NW_001495013]

223977

rs41256853

Non coding intronic

MBS007-1 - MBS043-1 D' = 0.06

431_A2 - MBS043-1 D' = 0.12

MBS030-1

[Genbank: NW_001494990]

1339300

rs17871971

Coding - first base in R codon

MBS043-1

[Genbank: NW_001495111]

1628598

rs29003967

Non coding intronic

013.sp6

[Genbank: NW_001495169]

651244

ss_182258871

Non coding intronic

013.sp6 - AH2-5 D' = 0.20

AH2-5

[Genbank: NW_001495205]

919203

rs41255759

Non coding intronic

MBS044-1

[Genbank: NW_001495330]

1925089

rs17870555

Non coding intronic

N/A

128.sp6

[Genbank: NW_001495453]

6360496

ss_182258880

Non coding intronic

N/A

004.sp6

[Genbank: NW_001495578]

257732

ss_182258869

Non coding

423_24 - 425_2 D' = 0.48

423_24 - 004.sp6 D' = 0.10

423_24

[Genbank: NW_001495569]

793596

ss_182258865

Non Coding

425_2 - 004.sp6 D' = 0.04

425_2

[Genbank: NW_001495569]

839251

ss_182258866

Non coding intronic

022.t7

[Genbank: NW_001492799]

128540

ss_182258873

Non coding intronic

Exclude SNP MBS031-1

MBS031-1

[Genbank: NW_001492799]

1124499

rs17871372

Coding - third base in C codon

055.t7

[Genbank: NW_001492961]

1632290

ss_182258877

Non coding

AH8-4 - 055.t7 D' = 0.02

AH8-4 - MBS015-1 D' = 0.21

AH8-4

[Genbank: NW_001492942]

738417

rs41255717

Non coding intronic

055.t7 - MBS015-1 D' = 0.09

MBS015-1

[Genbank: NW_001493001]

1324153

rs17871661

Non coding intronic

058.sp6

[Genbank: NW_001493063]

1152348

ss_182258883

Non coding

N/A

AH25-1

[Genbank: NW_001493148]

1355813

rs41257524

Non Coding

AH25-1 - MBS046-1 D' = 0.20

MBS046-1

[Genbank: NW_001493168]

1973152

rs41257490

Non coding intronic

436_C10

[Genbank: NW_001493182]

723654

ss_182258882

Non Coding

N/A

Bulge105

[Genbank: NW_001493378]

486637

ss_182258868

Non coding intronic

N/A

MBS018-1

[Genbank: NW_001493523]

2800849

rs41255724

Non coding intronic

N/A

105.sp6

[Genbank: NW_001493559]

10050072

ss_182258881

Non coding

105.sp6 - MBS033-1 D' = 0.07

105.sp6 - MBS021-1 D' = 0.41

MBS021-1

[Genbank: NW_001493612]

23880

rs17871403

Non Coding

MBS033-1 - MBS021-1 D' = 0.07

MBS033-1

[Genbank: NW_001493607]

941203

rs17871744

Non coding intronic

039.t7

[Genbank: NW_001493666]

1151813

ss_182258875

Non coding

039.t7 - MBS054-1 D' = 0.11

MBS054-1

[Genbank: NW_001493688]

831437

rs41257458

Non coding intronic

007.sp6

[Genbank: NW_001493983]

863397

ss_182258870

Non coding intronic

Bulge113 - 007.sp6 D' = 0.18

Bulge 113

[Genbank: NW_001493954]

1202924

ss_182258867

Non Coding

048.sp6

[Genbank: NW_001494027]

363121

ss_182258876

Non coding intronic

N/A

MBS025-1

[Genbank: NW_001494145]

446755

rs41255852

Non coding intronic

MBS025-1 - MBS035-1 D' = 0.05

MBS035-1

[Genbank: NW_001494172]

276736

rs17872223

Non coding intronic

MBS028-1

[Genbank: NW_001494262]

534627

rs17870274

Non coding intronic

N/A

070.t7

[Genbank: NW_001494320]

325234

ss_182258878

Non coding

MBS040-1 - 070.t7 D' = 0.05

MBS040-1

[Genbank: NW_001494295]

390532

rs17872131

Non coding intronic

090.t7

[Genbank: NW_001501727]

3153055

ss_182258879

Non coding

N/A

MBS041-1

[Genbank: NW_001494538]

322380

rs17870855

Non coding intronic

N/A