Jia-Xing Yue, Jing Li, Louise Aigrain, Johan Hallin, Karl Persson, Karen Oliver, Anders Bergström, Paul Coupland, Jonas Warringer, Marco Cosentino Lagomarsino, Gilles Fischer, Richard Durbin, Gianni Liti
Review posted on 23rd September 2016
1) It might be because this is a relatively recent posting, but I couldn't find the 15 Supplemental tables referred to in the manuscript file. Could you please post these supplemental files as part of the preprint subission if you haven't already?
2) The ENA accession for the PacBio data only has 10 strains in PRJEB7245, however 12 are reported in the manuscript. Could you please add the additional 2 PacBio datasets to PRJEB7245?
3) The ENA accession for the PacBio data does not appear to provide a mapping between yeast strain names and ENA sample accessions. Could you please post this information as a comment here and correct the sample accession in PRJEB7245 to include strain names?
4) Additional Ty1 insertions on ChrIII that are missing from the S. cerevisiae reference genome have been sequenced and reported previously in Hoang et al (2010): http://journals.plos.org/plosg.... It would be worth comparing your results to theirs and citing their paper for precedence if the new Ty loci are the same.