Skip to main content

Table 5 Effect of contig length and coverage on detection of SNPs and Indels

From: Gene discovery in the horned beetle Onthophagus taurus

 

Total detected SNPs

Total Detected Indels

 

Estimate

F1,38047

P

Estimate

F1,38047

P

Contig Length

1.73

4371

0.0000

0.128

138.8

<0.0001

Number Reads

0.96

5417

0.0000

0.313

3304

0.0000

  1. Both contig length (transformed) and number of reads (transformed) were related to total detected SNPs and total detected indels in standard least squares linear models. Residuals from these models were used in subsequent analyses to estimate levels of genetic variation in a contig controlling for sampling differences between contigs.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us