Mycoplasma contamination in the 1000 Genomes Project

Table 2 In our random download of The 1000 Genomes Project, 1944 high quality DNA measurements (i.e. no more than three bases with quality worse than 0.5) match Mycoplasma (with on average three or fewer mismatches) but do not match at all the reference human genome (bottom column 3)

	Type	High quality	Affected	Scans	Fraction
		Mycoplasma sequences	scans	downloaded	of scans
Pair	Ordinary	542	87	3454	3%
Pair	Colorspace	1042	63	145	43%
Single	Ordinary	234	78	384	20%
Single	Colorspace	126	41	75	55%
	Totals	1944	269	4058	7%

As with Table 1, column 4 gives the number of scans with at least one affected DNA measurement. The right most column gives the percentage of affected scans by type.

ISSN: 1756-0381