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 |
|
|
||||||||||
|
*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. |
||||||||||
|
Bontell et al. Genome Biology 2009 10:R53 doi:10.1186/gb-2009-10-5-r53 |
||||||||||
