Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain
Table 1
Predictions of functional consequences of SNPs and indels.
Consequences
SNPs
Novel SNPs
Indels
Novel indels
splice_donor_variant
29
9
2
0
splice_acceptor_variant
11
0
4
0
stop_gained
19
8
1
1
frameshift_variant
0
0
22
7
stop_lost
5
1
1
0
start_lost
11
3
2
0
missense_variant
2378
486
ā
0
inframe_insertion
0
0
28
2
inframe_deletion
0
0
26
2
splice_region_variant
1117
63
244
18
synonymous_variant
4238
281
0
0
stop_retained_variant
3
0
0
0
coding_sequence_variant
1
0
1
0
mature_miRNA_variant
4
2
2
0
5_prime_UTR_variant
1210
86
198
31
3_prime_UTR_variant
6563
484
1617
191
non_coding_transcript_exon_variant
11,955
640
2140
290
intron_variant
575,013
36,838
139,815
21,458
NMD_transcript_variant
42,052
2609
10,291
1372
non_coding_transcript_variant
143,110
8770
32,985
5190
upstream_gene_variant
96,888
8357
24,321
3992
downstream_gene_variant
93,184
5752
23,557
3390
intergenic_variant
224,557
13,198
48,568
8312
Consequences were predicted using Ensembl VEP and gene models from Ensembl version 76. Novel SNPs or indels are defined as variants that were not in MGP and dbSNP142 data sets.