Table 1 Genetic differences between RH-ERP and GT1

A. Summary of comparative genome sequencing between RH-ERP and GT1

Description

RH-ERP (parental)

RH-ERP F-P2 (mutant)

Total base pairs sequenced

6.1 × 10⁹

6.5 × 10⁹

Total paired end reads

4.0 × 10⁷

4.4 × 10⁷

Total reads aligned

3.7 × 10⁷

3.9 × 10⁷

Total reads aligned (%)

90.1

90.5

Human reads (%)

32.2

49.4

Toxoplasma gondii reads (%)

57.9

44.1

GT1 genome covered (%)

96.5

96.9

Reads in unassembled contigs (%)

0.9

0.7

Total Shared Variation Called

1,394

B. Genetic differences between RH-ERP and GT1

SNPs/indels within predicted coding regions

230

Nonsynonymous SNPs

133

Synonymous SNPs

43

Indels

54

SNPs/indels within predicted genes, outside coding regions

484

SNPs/indels in 1000 bp upstream of predicted ATG start (5′UTR)

SNPs/indels in 1000 bp downstream of predicted end codon (3′UTR)

133

143

SNPs/indels outside predicted genes

680

C. Functional enrichment in genetic differences between RH-ERP and GT1

Gene set

Enrichment in Gene Ontology function

P-value

Number of annotated genes with SNPs/indels

Percent of annotated genes with SNPs/indels in gene set (%)

Total number of genes annotated

Percent of annotated genes in genome (%)

Nonsynonymous SNPs and indels within predicted gene coding regions

3′5′-cyclic nucleotide phosphodiesterase

3.57^-03

3

2.19

16

0.24

Protein kinase

9.74^-03

7

5.11

120

1.75

ATP binding

0.02

11

8.03

270

3.93

SNPs/indels within 5′ UTR of predicted genes (1000 bp upstream of ATG start)

Nucleoside triphosphatase

8.47^-03

4

4.17

58

0.85

Nucleotide binding

0.01

5

5.21

103

1.50

ATPase activity

0.03

3

3.13

48

0.70