Comparison of whole genome sequencing performance from fish swabs and fin clips

BMC Research Notes

Table 2 Sequencing performance of fin clip, gill swab, and skin swab DNA extractions

	Fin clips	Skin swabs	Gill swabs
Number of samples	16	15	3
Total raw reads per sample	95,385,777 ± 3E + 7	100,620,434 ± 2E + 7	117,317,537 ± 1E + 7
Retained reads after quality filtering	95,375,602 ± 3E + 7	100,598,146 ± 2E + 7	117,304,915 ± 1E + 7
% of retained reads after filtering	99.99 ± 0.002%*	99.98 ± 0.02%*	99.99 ± 0.002%
Reads mapping to reference genome	70,226,556	71,256,195	85,762,531
% of mapped reads	73.75 ± 0.007%	70.47 ± 0.05%	73 ± 0.008%
Coverage	9.8 ± 2.8-fold	9.9 ± 1.8-fold	11.2 ± 1.2-fold
Read length	167.9 ± 3.5 bp	168.6 ± 7.3 bp	163.8 ± 2.0 bp

Means and standard deviation of seven different Qualimap summary statistics from the 16 fin clip-swab pairs: summaries from 16 fin clip, 3 gill swab, and 15 skin swab samples are presented. A significant p-value from Dunn’s multiple comparisons test (see Table 3) comparing the percentage of retained reads after quality filtering of skin swabs, gill swabs and fin clips is indicated with an asterisk. Only the comparison between skin swab and fin clip was significant
^*p < 0.05

ISSN: 1756-0500