Table 5 Details of the sequenced rare alleles obtained from this study and homology searches with Rice annotation Database

BDTG2

Xa1

Raghusail

HR575926

301

LOC_Os04g53120

NB-ARC domain containing protein, expressed

6.9e-56

zf-BED

PF02892.8

1.8e-12

BDTG10

Xa1

Raghusail

HR575924

893

LOC_Os04g53160

NBS-LRR disease resistance protein, putative, expressed

2.4e-66

zf-BED

PF02892.8

4.4e-07

IC524526

HR806763

701

AB002266

NBS-LRR disease resistance protein, putative, expressed

6.2e-82

zf-BED

PF02892.8

4.4e-07

BDTG11

Xa5

Raghusail

HR614233

158

LOC_Os05g01710

Transcription initiation factor IIA gamma chain, putative, expressed

5.0e-24

TFIIA_gamma_N

PF02268.9

5..2e-24

BDTG12

Xa5

Raghusail

HR575927

631

LOC_Os05g01710

Transcription initiation factor IIA gamma chain, putative, expressed

1.8e-11

TFIIA_gamma_N

PF02268.9

5..3e-24

Bangladeshi Patnai

HR614234

766

LOC_Os01g08330

Aspartic proteinase nepenthesin-1 precursor, putative, expressed

6.7e-05

Asp

PF00026.16

8.6e-25

BDTG13

Xa26

Bhasamanik

HQ832768

968

LOC_Os09g07440

Retrotransposon protein, putative, unclassified, expressed

3.4e-05

Plant_tran

PF04827.7

7.5e-10

BDTG18

Xa26

Lal Binni

HR806757

539

LOC_Os11g47000

Receptor-like protein kinase precursor, putative, expressed

1.0e-101

LRR_1

PF00560.26

0.47

Buhrimtui

HR806765

536

LOC_Os05g26090

Transposon protein, putative, CACTA, En/Spm sub-class

0.00042

-

-

-

Desi dhan

HR806766

532

LOC_Os11g47000

Receptor-like protein kinase precursor, putative, expressed

2.6e-101

LRR_1

PF00560.26

0.47

Raghusail

HR575921

490

LOC_Os11g36180

Receptor kinase, putative, expressed

1.8e-86

LRR_1

PF00560.26

0.26

BDTG 19

Xa27

Aijong

JM426578

638

LOC_Os08g37540

Retrotransposon protein, putative, Ty3-gypsy subclass, expressed

0.019

Transposase_28

PF04195.5

2.6e-101

Morianghou

JM426580

367

AY986493

Oryza sativa (indica cultivar-group) Xa27 (Xa27) mRNA, Xa27-IRBB27 allele, complete cds

2.3e-72

-

-

-

BDTG20

Xa21

Aijong

HR806747

542

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

3.7e-27

LRRNT_2

PF08263.5

5.9e-11

Bangladeshi Patnai

HR806741

188

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

8.6e-23

LRRNT_2

PF08263.5

5.9e-11

BDTG21

Xa21

IC524526

HR806762

530

LOC_Os11g36180

Receptor kinase, putative, expressed

4.9e-52

LRRNT_2

PF08263.5

2.3e-10

Bhasamanik

HR806751

451

LOC_Os11g36180

Receptor kinase, putative, expressed

4.9e-52

LRRNT_2

PF08263.5

2.3e-10

BDTG22

Xa21

Bangladeshi Patnai

HR806742

561

LOC_Os11g36180

Receptor kinase, putative, expressed

7.9e-115

LRRNT_2

PF08263.5

2.3e-10

BDTG24

Xa21

Bhasamanik

HR806749

678

LOC_Os11g36180

Receptor kinase, putative, expressed

3.8e-135

LRRNT_2

PF08263.5

2.3e-10

BDTG25

Xa21

Bangladeshi Patnai

HR806743

1 kb

LOC_Os11g36180

Receptor kinase, putative, expressed

6.2e-119

LRRNT_2

PF08263.5

2.3e-10

BDTG26

Xa21(A1)

IC524502

HR806759

248

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

3.4e-43

LRRNT_2

PF08263.5

2.3e-10

Raghusail

HR575925

268

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

3.7e-18

LRRNT_2

PF08263.5

5.9e-11

Aijong

HR806748

494

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

4.1e-29

LRRNT_2

PF08263.5

5.9e-11

Lal Binni

HR806755

515

LOC_Os04g17940

Retrotransposon protein, putative, unclassified, expressed

6.5e-28

RVT_1

PF00078.20

4.6e-26

Bhasamanik

HQ832770

457

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.2e-44

LRRNT_2

PF08263.5

5.9e-11

BDTG27

Xa21(A1)

Bangladeshi Patnai

HR806744

366

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.0e-39

LRRNT_2

PF08263.5

5.9e-11

Raghusail

HR575922

325

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

2.4e-48

LRRNT_2

PF08263.5

5.9e-11

BDTG28

Xa21(A1)

Bhasamanik

HR806752

359

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

LRRNT_2

PF08263.5

5.9e-11

BDTG29

Xa21(A1)

Bhasamanik

HR806750

377

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.6e-64

LRRNT_2

PF08263.5

2.6e-10

IC524526

HR806761

379

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

2.1e-63

LRRNT_2

PF08263.5

5.9e-11

Bangladeshi Patnai

HR806745

382

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.4e-62

LRRNT_2

PF08263.5

5.9e-11

Lal Binni

HR806756

387

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.1e-74

LRRNT_2

PF08263.5

5.9e-11

IC524502

HR806760

345

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.0e-37

LRRNT_2

PF08263.5

2.6e-10

BDTG30

Xa21(A1)

Gobindobhog

HR806764

323

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.1e-59

LRRNT_2

PF08263.5

5.9e-11

Bangladeshi Patnai

HR806746

328

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.9e-57

LRRNT_2

PF08263.5

5.9e-11

BDTG31

Xa21(A1)

Bhasamanik

HR806753

376

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

3.5e-74

LRRNT_2

PF08263.5

5.9e-11

Lal Binni

HR806758

384

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

4.8e-72

LRRNT_2

PF08263.5

5.9e-11

BDTG33

Xa21(A1)

Bhasamanik

HR806754

267

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

1.1e-13

BDTG34

Xa21(A1)

Raghusail

HR575923

279

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

2.5e-45

LRRNT_2

PF08263.5

5.9e-11

Gobindobhog

HR806767

347

LOC_Os11g35500

Receptor-like protein kinase 5 precursor, putative, expressed

3.2e-63

LRRNT_2

PF08263.5

5.9e-11