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Table 4 Summary of SNP effects in wild barley 454 transcripts

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

SNP effect B1K2 B1K30 B1K B1K2 B1K30 B1K B1K2 B1K30 B1K
In all regions (#) In genic region (%) Mean per genic region
Synonymous 1,514 1,225 3,943 45.49 32.63 28.81 2.411 1.284 1.298
Non-synonymous 699 564 1,919 21.00 15.02 14.02 1.113 0.591 0.632
3′ UTR 816 1,546 6,570 24.52 41.18 48.01 1.299 1.621 2.163
5′ UTR 154 149 458 4.63 3.97 3.35 0.245 0.156 0.151
Non-synonymous start 1 2 2 0.03 0.05 0.01 0.002 0.002 0.001
Start lost 0 1 1 0.00 0.03 0.01   0.001 0.000
Stop gained 8 14 27 0.24 0.37 0.20 0.013 0.015 0.009
1Splice site acceptor 2 3 10 0.06 0.08 0.07 0.003 0.003 0.003
2Splice site donor 3 6 13 0.09 0.16 0.09 0.005 0.006 0.004
Start gained 26 31 95 0.78 0.83 0.69 0.041 0.032 0.031
Intron 105 213 648 3.16 5.67 4.73    
3Upstream 753 1,041 3,445     0.746 0.70 0.785
4Downstream 1,504 1,942 7,381     1.489 1.31 1.682
Intergenic 1,173 1,272 3,854     0.167 0.223 0.213
Summary – SNPs with/in:     
5High/moderate impact 712 588 1,970     1.134 0.616 0.648
6Gene region 5,585 6,737 24,512       
7Genic region 3,328 3,754 13,686       
8CDS/exon regions 3,192 3,501 12,920       
9Gene with genic SNPs 628 954 3,039       
  1. 1Splice site acceptor: variant hits a splice acceptor site (two bases before exon start, except for the first exon).
  2. 2Splice site donor: variant hits a Splice donor site (two bases after coding exon end, except for the last exon).
  3. 3Upstream: variant hits Upstream of a gene (within length of 5Kb).
  4. 4Downstream: variant hits Downstream of a gene (within length of 5Kb).
  5. 5High/Moderate SNPs effect: nsSNP CDS + Spice acceptor + splice donor + start lost + stop gained.
  6. 6Gene region: Upstream +5 UTR + Exon + Intron +3 UTR + Downstream.
  7. 7Genic region: 5 UTR + Exon + Intron +3 UTR.
  8. 8CDS/exon region: 5 UTR + Exon +3 UTR.
  9. 9Number of genes with SNPs affecting the UTRs, exon and intron.
  10. SNP effects are based on mapping of 454 NR reads against chromosomal barley genome (Hv. 030312 v2.16).
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BMC Genomics

ISSN: 1471-2164

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