Rates of Allelic Dropout
MicroDrop was run twice, first on the pooled run output from CHIIMP, and
a second time on the manually quality filtered dataset. Each MicroDrop
analysis outputs individual and locus rates of allelic dropout. In the
first run of the pooled genotypes, the locus specific dropout rates
ranged from 0 (GLSA-22) to 48% (GLSA-52). Following manual processing
of genotypes the rates of dropout ranged from 0 (GLSA-22 and GS-4) to
36.3% (GLSA-52).
Dropout rates were also calculated for individual samples, and ranged
from 0 (HSU 1836, UMMZ 79760 and LACM 95619) to 40.58% (MVZ 2088), as
calculated from the pooled dataset (see Table 6 for a complete list).
HSU 8180 recovered a dropout rate of 14.73% and we found individual
replicates recovering shorter alleles where primer sequences were
clipped differentially, see Appendix 3 for specific details. Following a
manual evaluation of genotypes recovered across replicates, we
reevaluated the allelic dropout rates, which ranged from 0 (HSU 1836,
UMMZ 79760) to 100% in MVZ 5211 where all genotypes were missing. When
MVZ 5211 was removed the highest dropout recovered was in LACM 95619
with 77.3%. The LQMS had higher rates of dropout after manually
processing genotypes due to the removal of low confidence genotypes.