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. 2017 Jan 30;9(2):398–414. doi: 10.1093/gbe/evx005

Table 3.

Comparison of BWA Assembly with the Anolis and Gekko References

Species Reference Sequences
Anolis (160 seqs.)
Anolis trim Gekko (110 seqs.)
Gekko (110 seqs.)
Enrich. (%) Rec. (%) Comp. (%) Enrich. (%) Rec. (%) Comp. (%) Enrich. (%) Rec. (%) Comp. (%)
Tokay gecko 47.5 90.0 69.4 34.1 97.3 70.5 36.9 100 88.4
Giant day gecko 47.8 90.6 69.1 33.1 97.3 69.7 37.6 100 89.6
Reef gecko 53.4 90.6 65.6 38.3 99.1 65.8 43.0 100 84.3
Average 49.6 90.4 68.0 35.2 97.9 68.7 39.2 100 87.5

Note.––To make the comparison between the Anolis and Gekko reference even, the Anolis reference was trimmed to contain only the sequences present in the Snake reference (Anolis trim Gekko). Enrichment was measured as the percent of reads mapping to the reference (uncorrected for genome size). Recovery was calculated as the percent of the 165 targeted genes that had at least 5% completeness and that could be identified based on BLAST similarity and/or phylogenetic analysis. Completeness was calculated relative to the reference sequence for those genes identified as recovered using the BWA assembly method and the best reference for each gene. Abbreviations—Enrich., Enrichment; Rec., Recovery; Comp., Completeness.