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Table 2 Impact of INDELs on the GigaTON protein set

From: GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas

TYPE (alphabetical order)

Count

Percent

3’-UTR variant

32867

35.312 %

5’-UTR variant

12890

13.849 %

Chromosome number variation

15

0.016 %

Disruptive in-frame deletion

968

1.061 %

Disruptive in-frame insertion

502

0.539 %

Frameshift variant

5653

6.074 %

Frameshift variant + start lost

156

0.168 %

Frameshift variant + stop gained

84

0.09 %

Frameshift variant + stop lost

51

0.055 %

In-frame deletion

430

0.462 %

In-frame insertion

369

0.396 %

Intergenic region

39050

41.955 %

Start lost + disruptive in-frame deletion

3

0.003 %

Start lost + in-frame deletion

7

0.008 %

Start lost + in-frame insertion

1

0.001 %

Stop gained + disruptive in-frame deletion

1

0.001 %

Stop gained + disruptive in-frame insertion

1

0.001 %

Stop gained + in-frame insertion

7

0.008 %

Stop lost + in-frame deletion

1

0.001 %

  1. The INDELs have been annotated using snpEff v4.15 [22] using the transdecoder open reading frame annotations made on the contigs. The complete annotated vcf files for INDELs can be downloaded from the GigaTON website (ALL_INDEL.oysterAssembly1.0_annot1.vcf)