I used Micro-checker to assess my microsat amplification. I have 17 localities, of which 5 have null alleles. The null alleles are, however, not only in 1 or 2 microsats, but vary according to the locality. Hence, I do not want to discard the microsats in question, but am not sure how to proceed. Do I use the adjusted genotypes calculated by Microchecker to change these localities, and if so, how do I know which new genotype corresponds to which sample number, as Microchecker states "Genotypes are ordered by allele size. Note: Row numbers do not correspond to the original sample numbers".
Any help will be appreciated.
Regards
Genevieve
What do you want to do with the genotypes? For parentage analysis, we do calculations using both scenarios: either the observed homozygotes are truly homozygous, or observed homozygotes are heterozygous null, and then take the conservative result for parentage. E.g. If one of these methods gives a match, then consider the genotypes matching (or if using likelihood methods, take the one with the higher likelihood). This is done for each trio or pair being compared.
If you are doing some sort of population genetics, then you might just need allele frequencies (which micro-checker gives?).
I can't sign off without putting a plug in for genotyping by sequencing (GBS) methods which we think are a much better approach, at least for species without SNP chips available.
Hi Genevieve
IF a frequence of a null alleles top rate to 20% in a population for a microsatellite, it is more interesting to keep themselves espesialy in the genetic population study . To know the sample for which there was presence of null allele we are forced to go through a sequencing, but rather homozygous samples that are suspected by null alleles.
Callen et collaborateurs (1993)
Koorey et al., 1993
Chakraborty and colleagues (1992) propose to calculate the frequency of null alleles by evaluating a coefficient r they name.
r = D / (2-D)
D corresponding deficit of heterozygosity. This deficit is calculated by the equation:
D = (ht-hcd) / ht
- Badges
- Science topic
- Similar topics
- Phytochemistry
- Extracts