How can I access the Anopheles gambiae haplotype region sequences?


First a bit of background / warning: the alternative haplotype regions would actually be better described as alternative assemblies. The sequenced PEST strain is thought to have been segregating into two rather divergent versions/haplotypes for certain chromosome regions. The WGS sequencing reads will have come from both versions, and the assembly program seems to have generated two different assemblies for some of these regions. However, each of these alternative assemblies is likely to be a mosaic of segments from both versions, rather than representing a pure version of either 'haplotype'. The quality of these regions is sometimes quite poor (lots of gaps).

For example, go to the genome browser and in the "search for" box type "3L_hap_9:11046966-112165" and then click go, which corresponds to 3L:11046966-11206189. To see the latter, click on the red representation of the haplotype block and look in the pop-up box. Note that you can switch to a view of the alternative chromosome (i.e. with this alternative assembly region substituted) by taking the link in the pop-up. But we only have basic annotation (repeats, gaps, blast hits) on the alternative assembly regions. If you want the sequences to do your own alignment, you can use the 'Export data' link from the left-hand panel when you are viewing the region in Region in detail.