Low mean rho estimated by interval

[tahia]

Hi there

I am working on a diploid grass population and trying to estimate recombination rate by "interval" program. Since this population has three major genetic clusters, therefore, I tried to measure the recombination rate within each cluster separately.

As a test trial I chose one chromosome (~60 Mb) for 50 individuals from one genetic cluster (x2 chromosomes) and obtained SNPs with maf >0.1. I have tried with several densities of SNP (~1 SNP per 25 kb, 35 kb and 70 kb ) with theta=0.01 or 0.001 ( and -its 60000000 -samp 5000 -bpen 5).

Later, I've generated Mean rho by "start" with 200,000 burn in and checked the model convergence by "summary.interval" which looks fine. However, the mean rho I've got for all six combination of SNP density x theta seems relatively low compared to other plant species such as Rye or Barley. Attached is the mean rho plotted across the chromosome length with varying SNP density and theta. The x-axis jitter represents gene density across chromosome.

First I thought it might be an issue of the unit of loc file. I've checked the unit of loc file and it is indeed represented as Kb. Later, I've tried with two other genetic clusters and getting the similar trend of low estimates. It would be great if I could get an insight from you why I'm getting low estimated rho.

~Taslima