1. Basic processing

• 36 bp single-end Solexa reads

• ran Solexa pipeline using default parameters

• maq processing using default parameters

2. Data information

• samples

  • 2L: African - MW28, North American - Ral-303A, Ral-304A (MW - Malawi; Ral - Raleigh, NC)

  • X: African - MW6, North American - Ral-303A, Ral-304A

• range of bases (reference assembly 4)

  • 2L: 3Mbp - 4Mbp

  • X: 4Mbp - 5Mbp

• conversion of coordinates from assembly 4 -> 5

  • These regions were chosen partially because they easily map between assemblies 4 & 5

  • For 2L, from 3Mbp - 4Mbp the coordinates are exactly the same in v4 and v5

  • For X, at 4Mbp add 48,796 to v4 coordinates to get v5 coordinates (v4 4,000,000 = v5 4,048,796)

• coverage

  • These genomes were sequenced to 10x coverage

3. Synopsis of cns.view file - from http://maq.sourceforge.net/maq-manpage.shtml

• The MAQ command cns2view was used to create the cns.view files. These files give information for every base in the alignment.

• Column1 - chromosome

• Column2 - position (wrt to D. melanogaster reference sequence - v4)

• Column3 - reference base

• Column4 - consensus base

• Column5 - Phred-like consensus quality

• Column6 - read depth

• Column7 - the average number of hits of reads covering this position (this gives a measure of the uniqueness of a region - i.e. did the reads that were aligned here also map well to other locations)

• Column8 - the highest mapping quality of the reads covering the position

The following columns are probably not useful and may be incorrect anyway...

• Column9 - the minimum consensus quality in the 3bp flanking regions at each side of the site

• Column10- the second best call

• Column11- log likelihood ratio of the second best and the third best call

• Column12- and the third best call.