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Table 3 Summary of SNPs classification for different SNP sets

From: Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout

Functional Class SNPs with allelic imbalance 7.9 K % GATK/SAMtools Common SNPs 50.8 K % All putative SNPs 95.2 K %
Intergenic 2989 37.69% 20,356 40.00% 46,901 49.25%
 Intergenic(>5 K) 1633 20.59% 10,554 20.74% 27,651 29.03%
 Upstream (<5 K) 635 8.01% 4594 9.03% 9005 9.46%
 Downstream (<5 K) 721 9.09% 5208 10.23% 10,245 10.76%
Genic 4941 62.31% 30,529 60.00% 48,333 50.75%
 5’UTR 214 2.70% 1389 2.73% 2247 2.36%
 3’UTR 1677 21.15% 10,259 20.16% 16,420 17.24%
 CDS 2548 32.13% 15,178 29.83% 22,616 23.75%
 Intronic 502 6.33% 3703 7.28% 7050 7.40%
Non-synonymous 504 6.36% 3919 7.70% 5853 6.15%
 Stop gain 4 0.05% 50 0.10% 79 0.08%
 Missense 500 6.31% 3869 7.60% 5774 6.06%
LncRNA 684 8.63% 4386 8.62% 10,465 10.99%
Total number/percentage 7930 100.00% 50,885 100.00% 95,234 100.00%