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Table 2 SNP filtering criteria used in walnut SNP discovery

From: Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms

 

Item

Initial criteria

Adjusted

1

Minimum read depth mapped to the reference sequences (Minimum RMD)

≥ 5

 
 

Maximum read depth mapped to the reference sequences (maximum RMD)

No constraint

≤ 25 (+ 0.5- s)(a)

2

Folded variant frequency in SOLiD reads (FVF)

≥ 0.2

Statistically no deviation from 0.5(b)

3

Mapping quality score in SAMtools (MQS)

≥ 25

≥ 30

 

Reference SNP base quality

SNP base ≥40 for genic BESs and ≥45 for non-genic BESs

 

4

Removing homopolymer SNPs

SNP base string length ≥ 3 bp

 

5

Removing very close SNPs

> 3 bp between two contiguous SNPs

 

6

Removing SNPs at the right side of Sanger reads

> 30 bp away from the right side

 

7

Illumina genotyping quality

≥ 60 bp between two contiguous SNPs

 
  1. (a) See the text for definition of X ¯ and s. (b) See Methods.