The sequence.index file contains a list of all the sequence data produced by the project, pointers to the file locations on the ftp site and also all the meta data associated with each sequencing run.
For the phase 3 analysis the consortium has decided to only use Illumina platform sequence data with reads of 70 base pairs or longer. The analysis.sequence.index file contains only the active runs which match this criterion. There are withdrawn runs in this index. These runs are withdrawn because either: * They have insufficient raw sequence to meet our 3x non duplicated aligned coverage criteria for low coverage alignments. * After the alignment has been run they have failed our post alignment quality controls for short indels. * Contamination. * They do not meet our coverage criteria.
Since the alignment release based on 20120522, we have only released alignments based on the analysis.sequence.index