|
a)
| | | | |
|---|
|
Model term
|
Estimate
|
Standard error
|
z value
|
P
|
|---|
|
Pipeline
| | |
−0.348
|
0.728
|
|
CMiB
|
0
|
0
| | |
|
read2Marker
|
−0.1074
|
0.3090
| | |
|
Primer location
| | |
−0.513
|
0.6081
|
|
coding
|
0
|
0
| | |
|
others
|
−0.1590
|
0.3101
| | |
|
Sum of primer melting temperature
|
0.1420
|
0.1191
|
1.192
|
0.2333
|
|
Expected PCR product size
|
−0.0033
|
0.0015
|
−2.252
|
0.0244
|
|
b)
| | | | |
|
Model term
|
Estimate
|
Standard error
|
z
value
|
P
|
|
Pipeline
| | |
0.473
|
0.636
|
|
CMiB
|
0
|
0
| | |
|
read2Marker
|
0.0727
|
0.1536
| | |
|
SSR location
| | |
−1.486
|
0.137
|
|
coding
|
0
|
0
| | |
|
others
|
−0.2824
|
0.1901
| | |
|
Maximum No. of SSR repeats
|
0.1344
|
0.0233
|
5.782
|
7.39E-09
|
|
SSR motif (number of SSR repeat unit)
|
−0.0966
|
0.1534
|
−0.63
|
0.529
|
- PCR success was coded using a variable that took a value of 1 for success and 0 for failure. The primer melting temperature (Tm) was summed for both primers in a pair. The R functions called when estimating PCR success were: glm(formula = PCR.success ~ Pipeline + Primer.location + Sum.of.primer.Tm + Expected.PCR.product.size, family = binomial). The level of polymorphism was expressed in terms of number of alleles per locus (Na) and was analyzed using the following function calls in R: glm(formula = Na ~ Pipeline + SSR.location + Maximum.No..of.SSR.repeats + SSR.motif, family = poisson). SSR motif corresponded to the number of bases in the SSR repeat unit; di-, tri-, tetra-, hexa-, and penta-SSRs were coded as 2, 3, 4, 5 and 6, respectively.
