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

Table 5 Calculation of the MRCA of Ugandan type II and III isolates and reference strains based on the intron mutation rate

Chromosome	Intron length* (bp)	Minor SNPs in introns	MRCA Me49/UgII (years)	MRCA VEG/UgIII (years)
Type II
II	89,003	34	19,691
IV	85,471	58	34,979
VI	152,385	65	21,987
VIIa	198,902	28	7,256
IX	266,876	117	22,598
X	334,181	79	12,186
Total II	1,126,818	381	17,429
Type III
Ia	80,522	2		1,280
Ib	85,805	8		4,806
III	82,660	9		5,612
V	119,536	15		6,468
VIIb	220,517	39		9,116
VIII	337,557	78		11,911
XII	352,605	78		11,403
Total III	1,279,202	229		9,228

The divergence between Ugandan and reference strains were calculated based on the intron mutation rate 1.94 × 10^-8 [26]. A more comprehensive version is provided in Additional data file 4. *Length of intronic regions. MRCA, most recent common ancestor.

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