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Table 3 Prediction of the effects of variants

From: Comparative whole-genome analyses of selection marker–free rice-based cholera toxin B-subunit vaccine lines and wild-type lines

Impact (percentage in MucoRice-CTBs/WTs)

Effect type

Number of line-specific classified variants

50A

51A

55A

WT1

WT2

HIGH (1.4%/1.2%)

FRAME_SHIFT

5

8

12

10

5

SPLICE_SITE_ACCEPTOR

1

0

0

1

0

SPLICE_SITE_DONOR

2

0

0

0

0

START_LOST

0

0

0

0

0

STOP_GAINED

1

0

0

0

0

STOP_LOST

2

0

0

0

0

MODERATE (3.0%/1.7%)

CODON_CHANGE_PLUS_CODON_DELETION

0

1

1

0

2

CODON_CHANGE_PLUS_CODON_INSERTION

0

0

0

0

0

CODON_DELETION

2

1

5

1

5

CODON_INSERTION

0

1

0

0

0

NON_SYNONYMOUS_CODING

21

15

21

8

7

LOW (1.4%/1.3%)

NON_SYNONYMOUS_START

0

0

0

0

0

SPLICE_SITE_REGION

3

0

0

0

3

START_GAINED

3

1

0

1

0

SYNONYMOUS_CODING

13

4

7

7

7

SYNONYMOUS_STOP

1

0

0

0

0

MODIFIER (94.2%/95.8%)

DOWNSTREAM

307

237

337

205

323

INTERGENIC

395

305

404

250

407

INTRAGENIC

0

0

0

0

0

INTRON

30

31

40

29

56

UPSTREAM

8

6

10

7

4

UTR_3_PRIME

1

4

2

0

2

UTR_5_PRIME

3

5

3

5

5

  1. Line-specific variants (SNPs and InDels) that may affect protein function were categorized into 23 types. These types were further grouped into HIGH, MODERATE, LOW, and MODIFIER according to potential severity. The assignment criteria were pre-defined in the annotation program (SNPEff).