Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes

BMC Genomics

Table 1 Genome properties. Reads were either mapped to the Cryptosporidium parvum IowaII reference genome or assembled de novo using Spades

	Total sequence (Mbp)	Read length (bp)	Mapped reads (%)	Fraction of genome covered (%)	Sequencing coverage (X-fold +/− SD)	De Novo Genome Assembly Statistics			MDA statistics
	Total sequence (Mbp)	Read length (bp)	Mapped reads (%)	Fraction of genome covered (%)	Sequencing coverage (X-fold +/− SD)	Size (% of reference)	Longest contig (bp)	NG50	Ct (h)^a	Effic-iency^b	Yield (AU)^c
Cell 1	920	2 × 300	99.8 %	94.7 %	90.3 ± 157	91.8 %	225 980	57 459	2.3	70	0.85
Cell 2	1366	2 × 300	99.9 %	93.8 %	127 ± 225	90.7 %	227 055	64 805	3.0	65	0.74
Cell 3	2013	2 × 300	99.8 %	87.8 %	169 ± 540	80.6 %	147 412	20 114	3.0	123	1.69
Cell 4	341	2 × 300	99.6 %	69.4 %	30.6 ± 79.4	60.0 %	67 943	1 513	2.8	99	0.69
Cell 5	1218	2 × 300	99.8 %	74.9 %	105 ± 307	66.3 %	119 204	4 309	3.3	91	0.56
Cell 6	1460	2 × 300	99.9 %	68.4 %	111 ± 509	57.1 %	73 330	1 398	2.3	97	2.17
Cell 7	1470	2 × 300	99.8 %	78.8 %	90.3 ± 304	67.6 %	203 151	5 364	2.8	102	0.60
Cell 8	1460	2 × 300	99.8 %	85.5 %	112 ± 284	77.5 %	117 185	11 229	2.3	192	1.52
Cell 9	1360	2 × 300	99.8 %	94.9 %	118 ± 194	91.6 %	547 655	65 774	3.3	44	0.50
Cell 10	1877	2 × 300	99.8 %	66.9 %	115 ± 767	49.6 %	57 954	687	3.5	72	0.60
Meta-genome	6273	2 × 250	84.2 %	97.8 %	535 ± 829	94.4 %	95 102	7 076	N.A.	N.A.	N.A.

^aThe number of hours to reach above the background fluorescence threshold
^bThe exponential amplification of DNA in the exponential amplification phase where a value of 100 % represents a doubling in DNA concentration every 15 min
^cThe total DNA fluorescence (arbitrary fluorescence units) at the end of the 16 h MD

ISSN: 1471-2164