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

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

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

¹Aligned reads (%): proportion of all aligned reads, reads aligned 1x and over 1x.
²Gene: number of genes with SNPs.
Mapping against chromosomal barley genome (Hordeum vulgare 030312 v2.16) was used for SNP effect annotation.

ISSN: 1471-2164