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Table 2 Summary of SNPs showing ΔSNP-index from 0.6 to 1 within the candidate region

From: Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq

ΔSNP-index

Position

Ref

Alt

Mutated gene

Mutation Type

Gene Annotation

0.95

8,887,787

C

T

BGIOSGA024510

Missense (P to L)

metal transporter Nramp5

0.92

9,174,237

C

T

BGIOSGA024502

Intron mutation

GHD7 protein

0.57

2,570,339

G

A

BGIOSGA024818

5′-UTR mutation

Hypothetical protein

0.57

18,066,507

C

A

BGIOSGA025813

3′-UTR mutation

Hypothetical protein

0.57

19,252,302

T

A

BGIOSGA025883

Missense (R to W)

Hypothetical protein

0.97

7,743,062

G

A

None

/

/

0.84

6,051,970

T

A

None

/

/

0.76

16,841,982

G

T

None

/

/

0.6

4,343,274

G

A

None

/

/

  1. identified by MutMap analysis
  2. Ref: reference base in WT, Alt: altered base in the lcd1 mutant