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Table 3 Parameter estimates from best fitting model predicting frequencies of SNPs, transition and transversions in contigs

From: The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)

Parametera

Estimate

95% confidence limits

P

for estimating the number of SNPs

  
 

Intercept

−0.9828

−1.1137

−0.8520

< 0.0001

 

LENGTH

0.0002

0.0000

0.0003

0.0106

 

DEPTH

0.0146

0.0127

0.0165

< 0.0001

 

C/NC

−0.0999

−0.2136

0.0139

0.0854

for estimating the number of transitions (T i )

  
 

Intercept

−1.4039

−1.5489

−1.2588

< 0.0001

 

LENGTH

0.0001

0.0000

0.0003

0.0594

 

DEPTH

0.0139

0.0119

0.0158

< 0.0001

 

C/NC

−0.0398

−0.1683

0.0886

0.5435

for estimating the number of transversions (T v )

 
 

Intercept

−2.0007

−2.1868

−1.8147

< 0 .0001

 

LENGTH

0.0003

0.0001

0.0005

0.0006

 

DEPTH

0.0123

0.0099

0.0147

< 0.0001

 

C/NC

−0.1883

−0.3539

−0.0226

0.0259

  1. Estimates of variables from best fitting candidate model predicting the frequency of SNPs, transitions, and transversions in contigs (depth of 10 reads or more; length of 501 bp or longer).
  2. a LENGTH and DEPTH are the length and the depth of contigs, respectively, and C/NC is a dummy variable for the type of transcript (protein-coding (coded as 1) vs non-coding transcript (coded as 0)).