NCBI’s Sequence Read Archive contaminated with Mycoplasma

[Genohub]

~ 11% of NCBI’s Gene Expression Omnibus (GEO) projects between 2012 and 2013 contain at least ≥ 100 reads / million reads mapping to mycoplasma’s small 0.6 Mb genome: http://blog.genohub.com/mycoplasma-c...quencing-data/

- Genohub

[N311V]

Was that ~11% of GEO projects from cell cultures that had reads mapping to mycoplasma or ~11% of all GEO projects between 2012 and 2013 regardless of origin?

[Genohub]

Those were ~11% of GEO projects from cell cultures (see below). They mention that it's an underestimate because they discard mapped reads that were not just mycoplasma, but other bacteria too. If they lower their threshold to 10 mycoplasma mapped RPM, contamination rates were closer to 15%.

...."We estimated that 57% of the samples (n = 5328) were cultured and 43% (n = 4067)
were not (Supplemental Table 2). In series with cultured samples, 11% (52/484) had at least one sample with 100 or more reads per million (RPM) that mapped to mycoplasma"