Sceptical about SNP density in a locus

[Moeez-Ahmed-Khan-GE]

Hello,
My colleague utilised the tool found here to query the SNP density in a locus in gambiae (PEST) using the Ag1000 data set. There is a roughly 26 bp sequence (around the 4400 bp mark) with 0 variation in SNPs (red line) but not a very high conservation score (blue line) between different insect species (image attached). I did an alignment of this sequence with the Arabiensis genome and found that there are few nucleotide substitutions in Arabiensis reference genome relative to gambiae in this locus. The low species conservation has made me a little sceptical about the SNP density data. Specifically, how did the Ag1000 researchers ensure that closely related species like Arabiensis were not mistaken for gambiae? Also, could the low SNP density in that region be an artefact from sequencing. Pardon my naïveté as I am not a bioinformatician. Big fan of the project though!