Pipelines | CASAVA all | GATK all | ||||
---|---|---|---|---|---|---|
 |  | HRC |  | HRC | ||
 | Total | Total | HRC by CASAVA but not by GATK | Total | Total | HRC by GATK but not by CASAVA |
Total number of variant | 6082624 | 61497 | 409 | 6337108 | 63774 | 1349 |
TsTv Ratio | 2.00 | 2.09 | 1.88 | 1.88 | 2.03 | 1.07 |
Mendelian Violation | 290985 | 0 | 0 | 187920 | 0 | 0 |
In dbSNP | 5562308 | 60769 | 268 | 5609116 | 62277 | 643 |
In interGenic | 3682138 | 35416 | 257 | 3790849 | 36884 | 846 |
In CDS | 65785 | 650 | 2 | 64452 | 638 | 2 |
In ‘3 UTR | 77701 | 849 | 16 | 82211 | 853 | 11 |
In ‘5 UTR | 18552 | 240 | 0 | 20093 | 246 | 4 |
In Intronic | 4113210 | 47220 | 218 | 4412928 | 48805 | 818 |
In Non_coding_intronic | 214239 | 1826 | 26 | 217104 | 1839 | 40 |
In Exonic | 57842 | 580 | 1 | 56762 | 579 | 3 |
In Non_coding_exonic | 16356 | 110 | 0 | 15196 | 106 | 0 |
In Putative Promoter Region | 12780 | 135 | 0 | 15517 | 141 | 1 |
Non-Synonymous Coding | 19080 | 159 | 1 | 18299 | 161 | 2 |
Common Variant | 5395888 | 60389 | 205 | 5905677 | 62830 | 1335 |
Common Homozygougs Minor Variant in 1000genome | 4777175 | 56874 | 104 | 4792920 | 57620 | 194 |
Common Homozygougs Minor Variant in Q108 | 4727231 | 57643 | 142 | 4915274 | 60169 | 1293 |
Common Het (>5%) Variant in 1000genome | 4479609 | 56407 | 99 | 4494483 | 57151 | 189 |
Common Het(>5) Variant in Q108 | 4895168 | 59296 | 63 | 5422841 | 62027 | 1332 |