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Table 5 Comparison of several SNP filtering criteria and ADT design scores in true-positive and false-positive SNPs

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

SNP

No of SNPs

ADT design score

Average quality score of reference

SNP quality score of reference

SNP mapping quality score

Read mapping depth

Folded variant frequency

True-positive

2,765

0.974 ± 0.050(a)

54.9 ± 9.4

59.2 ± 6.6

34.3 ± 1.6

18.4 ± 9.3

0.39 ± 0.11

False-positive

2,655

0.971 ± 0.053

54.3 ± 10.1

59.1 ± 7.1

33.7 ± 2.0

31.7 ± 18.0

0.34 ± 0.11

P value of t test

 

0.0597

0.0136*

0.4553

<0.0001**

<0.0001**

<0.0001**

  1. (a) average ± standard deviation; * and ** represent statistical significance at 0.05 and 0.01 probability level, respectively.
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BMC Genomics

ISSN: 1471-2164

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