An analysis of publication data for 2009 identifies a total 5263 Wellcome-attribured articles in PubMed, of which 2313 are freely available in UKPMC. This indicates an overall open access compliance figure of around 44%.
Looking at the data more granularly, we can also see which journals are most used by Wellcome-funded authors.
In total, some 1113 journals published Wellcome-funded research in 2009 -- from Acta Crystallographica through to Zoones and Public Health -- with the top 10 titles (in terms of total number of articles published) publishing some 14% (733 articles) of the total "Wellcome research output".
As can be seen from the image above (click on it to make it legible), PLoS One was the title most used by Wellcome-funded researchers, publishing a total of 136 papers in 2009.