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There are lots of questions about how and why there is genetic variation between organisms of the same species, but I haven't been able to find a numerical value for the expected amount of genetic variation.

Let's say we have two different samples of MRSA252. We sequence these samples and get the full genomes of ~3 million base pairs each. What percentage of these bases would we expect to be different (assuming there is no sequencing error)? I figure it will be about 1%, but I haven't been able to find a source.

I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria. An academic source would be much appreciated.

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I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria.

Yes indeed it will. Bacteria are a huge domain of life; you might as well ask for variability between all plants or between all animals. Bacteria can live in very different environments, and the whole things is made more complex by widespread horizontal transfer.

Still, for bacteria, you can't do much better than E. coli, and boy are they a mess. Here's a paper from 2010 that blew my mind. The authors sequenced 61 E. coli genomes and found:

...that any given E. coli genome sequenced will have only roughly 20% of its genes part of the E. coli core, and the remaining 80% are not found in all other E. coli genomes.

20% variability within a species. 20%, one species. E.coli is an extreme example, but still, species is a stupid concept. Here's a 2006 paper finding that plenty of unique Campylobacter proteins simply aren't in plenty of Campylobacter species.

On a more broad scale, here's an excellent (and free) paper you should look at. It examines islands of "microdiversity" among various species, finding that some species are easily 50%-75% different. A simple way to estimate this is too look at gene number for bacterial species, which should make it clear that some of these bugs vary by up to an order of magnitude.

In short: A lot.

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There is a database of Multi Locus Sequence Typing (MLST) data for E. coli at http://mlst.ucc.ie/mlst/

These data are limited to sequences at seven genes: adk, fumC, gyrB, icd, mdh, purA and recA. Furthermore for each of these genes only part of the sequence (in the range 452-536 bp) is characterised.

Each strain tabulated is represented by a genotype consisting of the alleles present at each of these loci. There are many different alleles found for each locus ranging from 240 variants at recA to 431 variants at fumC.

I ran a pairwise comparison (87398 comparisons -nowhere near the maximum possible, but I didn't have time to let my script run all pairwise combinations) and found that the average total divergence at these loci was 1.3%

Although this is a very different perspective from the one described by @Amory, I think it is nicely complementary, and it reveals that even at genes shared by all strains of E.coli there is a degree of sequence divergence that is quite close to your guess of 1%.

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Thanks for the resource and info, this was really helpful. I accepted the other answer because there are links to a few papers. –  Tim Nov 3 '13 at 4:23

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