The most fundamental operation that MapSeq allows you to perform is viewing genotyping data for one or more samples of your choice, in any specific region of interest of the genome.

Please note that you will need viewing privileges to see the genotyping data for a number of samples. These privileges are usually granted by the investigator who submitted the samples (see more details here). However, a number of samples have publicly-viewable data, which you can freely browse.

The figure below shows an example of a genotyping data display. We show genotyping calls within the PfCRT gene, in a sample from Ghana (PF0001-C) and three reference samples (PG0001-C, PG0002-C and PG0003-C). The calls for each sample are arranged in a vertical column, and each horizontal row shows the calls at one specific variable position in the genome. The last column shows annotations for the position (in this case, showing that the positions are located within coding regions of PfCRT).

Genotyping calls are displayed in normal type when the allele is identical to that of the 3D7 reference we use for assembly. If the allele is different from reference, it is displayed on a coloured background.

At positions 458998-459003, the Ghanaian sample and one of the reference samples (ITA4) show a number of mutations, which are not present in the other two reference isolates (3D7 and HB3). These mutations are known to produce amino acid changes associated to resistance to chloroquine (CQ); therefore, their presence suggests that the first two samples are CQ-resistant. Note that MapSeq shows additional annotations at positions where mutations are known to cause phenotypic changes.

By using this simple functionality, it is possible to assess any sample of interest for the presence of mutations of interest. If you wish to know whether the call is well-supported, simply click on the call, and a popup will display the number of reads that were assembled to cover that position: in this case 41, which is a typical good coverage. If you want to further inspect the reads assembly, you can click on 'View Read Pileup' which will invoke LookSeq to show the deep sequencing reads.

Why not try this? Please follow the instructions in our simple tutorial .