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Table 2 Summary of reference-based mapping of wild barley reads against cultivated barley sequences

From: Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts

Reference → B1K30 Hv. fl-cDNA Barley HC genes Chr. Hv. WGS
Reads → B1K2 B1K2 B1K30 B1K B1K2 B1K30 B1K B1K2 B1K30 B1K
1 Aligned reads (%):
All 93.6 77.5 76.6 77 67.6 63 65.3 80.0 79.4 79.7
1x 52.7 47.1 47.5 47.3 51.8 48.6 50.2 32.7 35.7 34.2
>1x 40.9 30.3 29.2 29.7 15.8 14.4 15.1 47.3 43.7 45.5
SNPs:
Raw SNPs 28,289 27,279 24,637 40,639 16,284 14,509 24,446 39,545 36,021 61,852
Filtered SNPs 1,017 1,067 1,717 9,092 1,184 1,081 5,036 4,053 4,372 15,330
2Gene      132 299 1,805 1,010 1,488 4,389
SNPs/gene      9 3.6 2.8 4.0 2.9 3.5
SNPs/kb 4.4 3.5 2 1.78 7.3 2.8 2 3.5 2.6 2.4
  1. 1Aligned reads (%): proportion of all aligned reads, reads aligned 1x and over 1x.
  2. 2Gene: number of genes with SNPs.
  3. Mapping against chromosomal barley genome (Hordeum vulgare 030312 v2.16) was used for SNP effect annotation.