International Journal of Genomics / 2017 / Article / Tab 1

Research Article

Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain

Table 1

Predictions of functional consequences of SNPs and indels.

ConsequencesSNPsNovel SNPsIndelsNovel indels

splice_donor_variant29920
splice_acceptor_variant11040
stop_gained19811
frameshift_variant00227
stop_lost5110
start_lost11320
missense_variant23784860
inframe_insertion00282
inframe_deletion00262
splice_region_variant11176324418
synonymous_variant423828100
stop_retained_variant3000
coding_sequence_variant1010
mature_miRNA_variant4220
5_prime_UTR_variant12108619831
3_prime_UTR_variant65634841617191
non_coding_transcript_exon_variant11,9556402140290
intron_variant575,01336,838139,81521,458
NMD_transcript_variant42,052260910,2911372
non_coding_transcript_variant143,110877032,9855190
upstream_gene_variant96,888835724,3213992
downstream_gene_variant93,184575223,5573390
intergenic_variant224,55713,19848,5688312

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.