negative SNP?

[biocc]

hi, I used novoalign and BWA to map short reads, and got some mutation. when i use Tablet to visualize the alignment, some it may be negative SNP. right?

dsm1731_genome_3940680 185328 . A G 17.1 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=3,8,8,0;MQ=56;PV4=0.0034,3.9e-08,0.0011,1 PL:GT:GQ 47,0,234:0/1:50


dsm1731_genome_3940680 185328 A R 82 82 56 19 TGT,GG,,,.G,GGGG,.^~. +1$II+IIIIIIID71III

the attach file is the visualization.

[maubp]

It looks like it could be a A/G SNP, but all the reads supporting the SNP appear to have at least four other mismatches - and there some patterns here (e.g. three bases before your SNP and two bases after it).