Table 1 Summary of 454 whole genome sequencing output and SNP identification of a type II/III recombinant T. gondii strain
Number | Chromosome length (bp) | Number of reads* | Total contig length (bp) | Coverage by contigs | Average reads/kb | Type II SNPs* (Green†) | Type III SNPs‡ (Blue†) | Novel SNPs§ (Orange†) | Major SNP¶ density/kb | Minor SNP¥ density/kb |
|---|---|---|---|---|---|---|---|---|---|---|
Ia | 1,896,408 | 20,649 | 1,585,140 | 83.59% | 13.03 | 2 | 128 | 7 | 0.067 | 0.005 |
Ib | 1,956,324 | 20,583 | 1,639,876 | 83.82% | 12.55 | 1 | 1,483 | 10 | 0.758 | 0.006 |
II | 2,302,931 | 24,968 | 1,939,495 | 84.22% | 12.87 | 4,370 | 73 | 52 | 1.898 | 0.054 |
III | 2,470,845 | 26,771 | 2,060,909 | 83.41% | 12.99 | 27 | 4,224 | 73 | 1.710 | 0.040 |
IV | 2,576,468 | 27,510 | 2,150,897 | 83.48% | 12.79 | 4,731 | 176 | 60 | 1.836 | 0.092 |
V | 3,147,601 | 33,619 | 2,582,080 | 82.03% | 13.02 | 54 | 5,725 | 26 | 1.819 | 0.025 |
VI | 3,600,655 | 39,723 | 3,042,491 | 84.50% | 13.06 | 1,985 | 168 | 99 | 0.551 | 0.074 |
VIIa | 4,502,211 | 48,365 | 3,797,608 | 84.35% | 12.74 | 8,663 | 79 | 56 | 1.924 | 0.030 |
VIIb | 5,023,822 | 53,768 | 4,231,651 | 84.23% | 12.71 | 62 | 5,530 | 41 | 1.101 | 0.021 |
VIII | 6,923,375 | 75,308 | 5,851,305 | 84.52% | 12.87 | 123 | 6,775 | 158 | 0.979 | 0.041 |
IX | 6,384,456 | 72,298 | 5,337,365 | 83.60% | 13.55 | 8,119 | 325 | 269 | 1.272 | 0.093 |
X | 7,418,475 | 85,205 | 6,298,377 | 84.90% | 13.53 | 13,459 | 236 | 209 | 1.814 | 0.060 |
XI | 6,570,290 | 70,653 | 5,549,592 | 84.46% | 12.73 | 49 | 60 | 117 | - | 0.034 |
XII | 6,871,637 | 74,458 | 5,770,139 | 83.97% | 12.90 | 58 | 4,809 | 75 | 0.700 | 0.019 |
Total | 61,645,498 | 673,878 | 51,836,925 | 84.09% | 13.00 | 41,703 | 29,791 | 1,252 | 1.264 | 0.042 |