heterozygosity rate

[joxcargator73]

I am trying to have an idea of the level of heterozygosity in a genome of 50 Mb that I just assembled. Assembly with 250 PE MySeq
I tried botiew2 to re-map high quality pair end-reads to my contigs. Them using sam tools created a bam sorted and indexed file. Finally SNPs were called using freebayes. I filtered for Quality >20 and called only for SNPs.
My vcf file contains more than 100,000 SNPs. I believe that some how I am over estimating the number of SNPs. Maybe I am missing something.
Besides a couple of reports http://www.nature.com/ncomms/2013/13...ncomms3673.pdf) I do not have others to compare the level of SNPs I have obtained.
Any comments about this result will be appreciated

[Brian Bushnell]

It depends on the organism, but they can have SNP rates of 1/1000 (like human) or less... or as many as 1/100 or more. 100k SNPs in a 50Mbp diploid genome is not surprising.

[joxcargator73]

Thanks. YES the organism is a oomycete. Usually highly heterozygous. Actually there the filtered VCF file contains 545,000 SNPS