Table 3 Quality of whole genome sequences generated directly from stools containing C. hominis and C. parvum
Isolate; species and gp60 subtype; BioProject number | Total # base pairs sequenced (after merging reads) | Total # base pairs mapped to reference sequence | Proportion of Cryptosporidium DNA compared to background | % of reference genome covered | Mean depth on reference sequence | % AT content of reads mapped to reference sequence |
|---|---|---|---|---|---|---|
Pilot phase | Â | Â | Â | Â | Â | Â |
 UKH3 (IMS preparation) | 337,791,948 | 305,024,423a | 90.30 % | 98 % | 34.71 × | 67.49 % |
 C. hominis IbA10G2 | ||||||
 PRJNA253834 | ||||||
 UKP2 (IMS preparation) | 510,081,295 | 471,881,392b | 92.51 % | 100 % | 51.80 × | 67.92 % |
 C. parvum IIaA19G1R2 | ||||||
 PRJNA253836 | ||||||
 UKP2 (CsCl preparation) | 521,277,984 | 426,692,177b | 81.86 % | 100 % | 46.84 × | 67.85 % |
 C. parvum IIaA19G1R2 | ||||||
 PRJNA253836 | ||||||
Main phase | Â | Â | Â | Â | Â | Â |
 UKH4 | 2,164,426,378 | 1,828,866,488a | 84.50 % | 96 % | 209.17 × | 62.72 % |
 C. hominis IaA14R3 | ||||||
 PRJNA253838 | ||||||
 UKH5 | 2,182,317,271 | 1,765,458,438a | 80.90 % | 96 % | 201.92 × | 63.03 % |
 C. hominis IbA10G2 | ||||||
 PRJNA253839 | ||||||
 UKP3 | 1,703,132,267 | 1,514,828,932b | 88.94 % | 99 % | 166.42 × | 63.55 % |
 C. parvum IIaA18G2R1 | ||||||
 PRJNA253840 | ||||||
 UKP4 | 1,967,147,533 | 1,751,979,030b | 89.06 % | 99 % | 192.48 × | 63.60 % |
 C. parvum IIaA15G2R1 | ||||||
 PRJNA253843 | ||||||
 UKP5 | 288,922,509 | 244,528,063b | 84.63 % | 99 % | 26.86 × | 67.67 % |
 C. parvum IIaA15G2R1 | ||||||
 PRJNA253845 | ||||||
 UKP6 | 1,169,379,989 | 954,176,437b | 81.60 % | 99 % | 104.83 × | 67.73 % |
 C. parvum IIaA15G2R1 | ||||||
 PRJNA253846 | ||||||
 UKP7 | 795,715,168 | 708,613,859b | 89.05 % | 99 % | 77.85 × | 63.64 % |
 C. parvum IIaA17G1R1 | ||||||
 PRJNA253847 | ||||||
 UKP8 | 1,896,616,473 | 1,587,380,412b | 83.70 % | 98 % | 174.39 × | 63.20 % |
 C. parvum IIdA22G1 | ||||||
 PRJNA253848 |