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
| | | | | | |
- 1Splice site acceptor: variant hits a splice acceptor site (two bases before exon start, except for the first exon).
- 2Splice site donor: variant hits a Splice donor site (two bases after coding exon end, except for the last exon).
- 3Upstream: variant hits Upstream of a gene (within length of 5Kb).
- 4Downstream: variant hits Downstream of a gene (within length of 5Kb).
- 5High/Moderate SNPs effect: nsSNP CDS + Spice acceptor + splice donor + start lost + stop gained.
- 6Gene region: Upstream +5 UTR + Exon + Intron +3 UTR + Downstream.
- 7Genic region: 5 UTR + Exon + Intron +3 UTR.
- 8CDS/exon region: 5 UTR + Exon +3 UTR.
- 9Number of genes with SNPs affecting the UTRs, exon and intron.
- SNP effects are based on mapping of 454 NR reads against chromosomal barley genome (Hv. 030312 v2.16).