Table 1. INDELs counts.
| described in ENSEMBL | described in 1000 Genome only | novel | total per consequence | |||||||||
| consequence | average (std.dev) | average rare (std.dev) | Ratio rare/total | average (std.dev) | average rare (std.dev) | Ratio rare/total | average (std.dev) | average rare (std.dev) | average rare complex | Ratio rare/total | average | rare |
| ESSENTIAL_SPLICE_SITE | 5.25 (1.43) | 0.24 (0.44) | 0.045714286 | 0.34 (0.52) | 0.07 (0.26) | 0.205882353 | 0.61 (0.84) | 0.43 (0.68) | 0.38 (0.65) | 0.704918033 | 6.2 | 0.74 |
| STOP | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0.03 (0.21) | 0.03 (0.21) | 0.02 (0.19) | 1 | 0.03 | 0.03 | ||
| COMPLEX_INDEL | 3.13 (1.01) | 0.17 (0.41) | 0.054313099 | 0.36 (0.52) | 0.09 (0.29) | 0.25 | 0.47 (0.63) | 0.24 (0.43) | 0.21 (0.41) | 0.510638298 | 3.96 | 0.51 |
| FRAMESHIFT_CODING | 69.4 (7.38) | 3.24 (2) | 0.046685879 | 3.28 (1.73) | 1.15 (1.05) | 0.350609756 | 23.49 (5.43) | 15.73 (4.89) | 13.81 (5.51) | 0.670940171 | 96.17 | 20.11 |
| NON_SYNONYMOUS_CODING | 68.33 (6.57) | 2.59 (1.8) | 0.037920937 | 2.24 (1.11) | 0.47 (0.67) | 0.209821429 | 6.69 (3.19) | 6.08 (3.13) | 5.2 (3.07) | 0.908819133 | 77.26 | 9.13 |
| SPLICE_SITE | 98.42 (7.53) | 3.35 (2.15) | 0.034044715 | 4.69 (2.01) | 0.97 (0.99) | 0.206823028 | 7.05 (3) | 5.21 (2.74) | 4.84 (2.68) | 0.739007092 | 110.16 | 9.53 |
| 5PRIME_UTR | 22.78 (3.18) | 0.66 (0.92) | 0.02907489 | 0.53 (0.64) | 0.14 (0.35) | 0.264150943 | 1.37 (1.12) | 1.37 (1.12) | 1.28 (1.08) | 1 | 24.69 | 2.17 |
| 3PRIME_UTR | 49.45 (5.3) | 1.32 (1.28) | 0.026720648 | 3.08 (1.45) | 0.4 (0.59) | 0.12987013 | 2.33 (1.68) | 2.18 (1.67) | 2.05 (1.63) | 0.935622318 | 54.85 | 3.9 |
| INTRONIC | 616.76 (32.95) | 16.44 (9.63) | 0.026623377 | 32.93 (5.55) | 6.33 (2.71) | 0.192401216 | 37.69 (11.25) | 27.6 (10.81) | 25.2 (10.8) | 0.734042553 | 687.38 | 50.37 |
| OTHER | 12.91 (2.58) | 0.6 (0.74) | 0.046511628 | 0.36 (0.53) | 0 (0) | 2.02 (1.32) | 0.85 (0.96) | 0.78 (0.93) | 0.420792079 | 15.29 | 1.45 | |
| total per category | 946.42 | 28.61 | 0.030232558 | 47.81 | 9.61 | 0.201046025 | 81.76 | 59.72 | 53.77 | 0.730722154 | ||
The table summarises the counts and standard deviation of INDELs according to their predicted consequence in the full dataset, in the subgroups of rare variants (i.e. MAF<0.05) and for the novel calls also the rare variants as calculated by excluding the familial cases from the dataset and re-computing the MAF. Adjusted p value indicates the results of a Wilcoxon test between rare variants in the entire dataset, and those rare in the dataset without familial cases.