Table 3 Summary of SNPs classification for different SNP sets
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% |