Table 4

Characteristics of the eight SNP markers surrounding the GPC-B1 locus

Unigene

Type1

Informative base

12-fold2

16-fold2

Assay

Maq-default

Maq-120

Brachypodium

Rice

Sorghum

RPKM3

High Bulk

Low Bulk

BFR


Ta#S22380117

H

LDN

YES

YES

SSCP

YES

YES

3g03160

02g04330

04g002930

1.97

0.059

0.226

3.84

Ta#S18006314

S

-

NO

NO

SSCP

YES

NO

3g03270

02g04460

04g002980

51.72

0.255

0.832

3.27

Ta#S16259088

S

-

YES

YES

SSCP

YES

YES

3g03340

02g04500

04g003030

19.92

0.034

0.965

28.46

Ta#S37941845

H

LDN

YES

YES

KASPar

NO

YES

3g03330

02g04490

04g003020

29.92

0.130

0.861

6.60

Ta#S17984935

H

LDN

YES

YES

SSCP

YES

YES

-

02g04650

04g003150

28.85

0.075

0.436

5.84

Ta#S32700697

H

RSL65

YES

YES

KASPar

NO

YES

3g03530

02g04660

04g003160

19.36

0.397

0.017

23.00

Ta#S13163314

H

LDN

YES

YES

KASPar

NO

YES

1g39300

06g30910

10g020020

2.99

0.015

0.230

15.17

Ta#S17985476

H

RSL65

YES

YES

SSCP

YES

YES

3g03480

03g59470

01g004030

23.63

0.156

0.022

7.19


1 H = hemi-SNP, S = simple SNP

2 SNP present in Maq-120 analysis using 12× and 16× coverage

3 RPKM: reads per kilobase per million mapped reads

Trick et al. BMC Plant Biology 2012 12:14   doi:10.1186/1471-2229-12-14

Open Data