Mycoplasma contamination in the 1000 Genomes Project

Table 1 Approximately 8% of The 1000 Genomes Project was selected at random and downloaded

	Type	Mycoplasma	Affected	Scans	Fraction
		sequences	scans	downloaded	of scans
Pair	Ordinary	797	106	3454	3%
Pair	Colorspace	17 015	111	145	77%
Single	Ordinary	752	108	384	28%
Single	Colorspace	4 020	72	75	96%
	Totals	22 584	397	4058	10%

Of the 53 billion DNA measurements down loaded, 22584 (bottom column 3) match Mycoplasma (with on average three or fewer mismatches) but do not match at all the reference human genome GRCh37.p5. Typically samples infected with Mycoplasma are immediately destroyed. Column 4 gives the number of scans with at least one affected DNA measurement. The final column gives this as a percentage of scans of the same type.

ISSN: 1756-0381