The chr 11 and chr 20 alignment files are put in place to give the 1000 Genomes analysis group a small section of the genome to run test analyses on before committing to a particular strategy to run across the whole genome. Everything in the chr 11 and chr 20 files is also represented in the mapped bam file. To get a complete view of what data we aligned you only need to download the mapped and unmapped bams, the chr 11 and chr 20 bams are there as a convenience to the analysis group.