Skip to main content

Table 1 Summary of 454 whole genome sequencing output and SNP identification of a type II/III recombinant T. gondii strain

From: Whole genome sequencing of a natural recombinant Toxoplasma gondiistrain reveals chromosome sorting and local allelic variants

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
  1. *SNPs denoting a type II background. TgCkUg2 is identical to Me49, but different from VEG. The colors correspond to the colours used for the respective SNP types in Figures 1 and 2 and Additional data files 1 and 2. SNPs denoting a type III background. TgCkUg2 is identical to VEG, but different from Me49. §SNPs where TgCkUg2 has a novel allele, different from both Me49 and VEG. The predominant SNP type, corresponding to the chromosomal background type. ¥SNPs where TgCkUg2 differs from the background type, including novel SNPs.