Table 10.
Frequencies of SNPs by function and chromosome.
| I | II | III | IV | V | X | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4856 | 4858 | 4856 | 4858 | 4856 | 4858 | 4856 | 4858 | 4856 | 4858 | 4856 | 4858 | |
| Function | ||||||||||||
| Exon | ||||||||||||
| Insert |
9,942 | 91 | 16,423 | 334 | 10,263 | 156 | 11,219 | 6 | 8,645 | 112 | 11,106 | 437.11 |
| Deletion | 13825.97 | 78.05 | 17536.07 | 320.82 | 13684.02 | 192.04 | 15121.4 | 5.6 | 13436 | 93.73 | 11907.1 | 309.85 |
| bs | 19107.81 | 4110.87 | 41335.02 | 21232.1 | 19126.52 | 11330.5 | 12926.4 | 173.73 | 45618 | 1944.89 | 11563.6 | 6003.35 |
| syn | 9165.53 | 2406.68 | 19484.52 | 10292 | 7775.01 | 6870.87 | 5243.72 | 106.48 | 23642 | 876.37 | 5839.05 | 3192.57 |
| Total | 42876.05 | 4279.99 | 75293.76 | 21886.6 | 43073.55 | 11679.1 | 39267 | 184.94 | 67698 | 2151.1 | 34576.3 | 6750.32 |
| Intron | ||||||||||||
| Insert | 26409.16 | 435.8 | 20319.57 | 782.81 | 8397.01 | 867.75 | 13536.1 | 16.81 | 19268 | 201.52 | 14540.4 | 459.24 |
| Deletion | 11806.45 | 305.71 | 22268.03 | 648.06 | 26590.53 | 654.37 | 23657.7 | 16.81 | 11769 | 126.54 | 15570.8 | 520.11 |
| bs | 19263.15 | 5281.69 | 31731.94 | 14167.6 | 14306.02 | 10605 | 16828.7 | 173.73 | 36974 | 2371.36 | 14998.3 | 6877.58 |
| Total | 57478.76 | 6023.21 | 74319.54 | 15598.4 | 49293.56 | 12127.2 | 54022.6 | 207.36 | 68011 | 2699.41 | 45109.5 | 7856.92 |
| UTR | ||||||||||||
| Insert | 11495.75 | 695.99 | 21850.5 | 1803.03 | 11507.01 | 1322.96 | 8536.29 | 44.83 | 19789 | 243.7 | 7785.4 | 586.5 |
| Deletion | 24,079 | 852 | 17,675 | 1,655 | 23,325 | 1,046 | 15,487 | 22 | 16,456 | 248 | 18,662 | 580.97 |
| bs | 23457.55 | 6036.22 | 25747.41 | 18421.7 | 15239.02 | 11842.7 | 13658.1 | 263.4 | 31558 | 3791.37 | 10876.7 | 7137.63 |
| Total | 59032.24 | 7584.3 | 65273.15 | 21880.2 | 50071.06 | 14211.2 | 37681.6 | 330.65 | 67802 | 4283.45 | 37324.1 | 8305.1 |
| IG | ||||||||||||
| Insert | 23923.59 | 1144.8 | 28670.08 | 3054.24 | 11351.51 | 1856.42 | 27194.2 | 140.11 | 38432 | 328.05 | 34805.3 | 1593.52 |
| Deletion | 59032.24 | 787.05 | 44814.4 | 2771.91 | 23791.53 | 1593.25 | 58290.7 | 117.69 | 53950 | 313.99 | 49689.2 | 1659.91 |
| bs | 34021.21 | 9997.48 | 54556.66 | 39538.3 | 32966.04 | 20420.6 | 41827.8 | 1333.8 | 84675 | 5740.94 | 43277.7 | 22901.3 |
| Total | 116977.1 | 11929.33 | 128041.2 | 45364.4 | 68109.09 | 23870.2 | 127313 | 1591.6 | 177057 | 6382.99 | 127772 | 26154.7 |
The numbers represent isolate × 10-8 SNPs per base. *
*For ease in comparison of frequencies across categories and strains, we divided the number of polymorphisms by the number of analyzed sites and multiplied that number by 108. For example, the proportion of insertion polymorphisms in CB4856 is 9942*10-8.