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Table 3 Quality of whole genome sequences generated directly from stools containing C. hominis and C. parvum

From: Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples

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       
 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       
 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
  1. amapped against C. hominis TU502 v1 reference sequence (Bioproject PRJNA15585)
  2. bmapped against the C. parvum IOWA II v1 reference sequence (Bioproject PRJNA15586) using default mapping conditions