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Table 3 WGS variants Identified in 30x Coverage of a Persian Cat PRA Trio

From: Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7

   

Analysis typeb

  

Variant impacta

Functional Class

WGS trio

Trio Segregation

RetNet genes

GWAS haplotype

High

Stop gain

379

11

6

1

 

Start/Stop loss

85

5

2

-

 

Splice donor/acceptor

1262

9

9

1

 

Exon deletion

2

-

-

-

 

Frameshift

2254

18

20

4

 

Rare amino acid

-

-

-

-

Moderate

Codon alteration

971

15

11

4

 

Missense

35,444

1014

544

41

 

Splice branch

-

-

-

-

 

5′ or 3′ UTR Deletion

1

-

-

-

Low

 

64,791

2072

1155

105

Modifier

 

16,876,221

538,148

87,816

11,018

  1. aImpact determined by snpEff as defined by http://snpeff.sourceforge.net/SnpEff_manual.html#eff. b The analyses is based on feline reference genome sequence (V6.2). Effect counts are higher than variant counts because they include the effects of each alternate allele on each nearby gene isoform. GWAS haplotype are the variants identified within the haplotype region. For Trio Segregation, the variants segregated with the disease phenotype as well, not just parent to offspring
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BMC Genomics

ISSN: 1471-2164

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