Table 2 Summary statistics of the identified variants
From: Variant discovery in the sheep milk transcriptome using RNA sequencing
Fields | Counts SnpEff | Counts VEP | |
|---|---|---|---|
Variants processed | 216637 | 212742 | |
SNPs | 197948 | 195503 | |
Insertions | 8603 | 7233 | |
Deletions | 10086 | 9032 | |
Effects by impact | |||
HIGH | 2128 | 1891 | |
MODERATE | 22440 | 22385 | |
LOW | 43986 | 43667 | |
MODIFIER | 312170 | 232768 | |
Effects by type | |||
3_prime_UTR | 12940 | 12950 | |
5_prime_UTR | 1819 | 1824 | |
downstream_gene | 113225 | 113207 | |
frameshift | 1162 | 1096 | |
inframe_deletion | 168 | 314 | |
inframe_insertion | 127 | 229 | |
intergenic_region | 96639 | 16991 | |
intron | 59198 | 58408 | |
missense | 21841 | 21824 | |
non_coding_exon | 2002 | 1993 | |
non_coding_transcript | 10 | 9492 | |
splice_acceptor | 525 | 332 | |
splice_donor | 594 | 371 | |
splice_region | 2353 | 2187 | |
start_lost | 16 | 28 | |
stop_gained | 119 | 112 | |
stop_lost | 28 | 30 | |
stop_retained | 26 | 31 | |
synonymous | 43003 | 43004 | |
upstream_gene | 27952 | 27948 | |