Without primers = 215 bp
Appendix 5: Identification of size homoplasy in samples UMMZ
79760 and HSU 1836 at GLSA-52 from the bioinformatically pooled dataset.
UMMZ 79760 is truly homozygous, while HSU 1836 is not. There also seems
to be different polymorphisms (highlighted in yellow) in all three
alleles even though they are all 255 bp fragments.
From the Methods Combined data:
- Samples: UMMZ 79760 and HSU 1836
- Locus: GLSA-52
- Primers
> UMMZ79760 GLSA52-GLSA52_1 255bp
allele/locus/total=473/6292/23088
TCCATCCACAGTGTGTGAGCCTGTGCGCGCGTGCACACACACACACACACACACACACACACACAGAGGACAGATGTTCTCCTGCAGCTCCTGCTCCTGTGGTGTCCTCTCTCTGTACAAGACTAGGAAACAAAGGTGTGACATCAGCTGAATGTCCACAGCCAAGAGTGACAAACTAACACAACTGCACAGAGCAAGGGGCACAGGACAGGTGCTCACCCGCTTCAGGGTCCCCATGCTTGAGTGGACTCCAGG
>HSU1836 GLSA52-GLSA52_1 255bp
allele/locus/total=948/10535/26164
TCCATCCACAGTGTGTGAGCCTGTGCACGCGTGCACACACACACACACACACATACACACACACAGAGGACAGATGTTCTCCTGCAGCTCCTGCTCCTGTGATGTCCTCTCTCTGTACAAGACTAGGAAACAAAGGTGTGACATCAGCTGAATGTCCACAGCCAAGAGTGACAGACTAACACAACTGCACAGAGCAAGGGGCACAGGACAGGTGCTCACCCGCTTCAGGGTCCCCATGCTTGAGTGGACTCCAGG
>HSU1836 GLSA52-GLSA52_2 255bp
allele/locus/total=571/10535/26164
TCCATCCACAGTGTGTGAGCCTGTGCGCGCGTGCACACACACACACACACACACACACACACACAGAGGACAGATGTTCTCCTGCAGCTCCTGCTCCTGTGATGTCCTCTCTCTGTACAAGACTAGGAAACAAAGGTGTGACATCAGCTGAATGTCCACAGCCAAGAGTGACAAACTAACACAACTGCACAGAGCAAGGGGCACAGGACAGGTGCTCACCCGCTTCAGGGTCCCCATGCTTGAGTGGACTCCAGG
Appendix 6: Cost Calculations
Qiagen QiaAmp Mini Kit (Qiagen.com #51304): $170 for 50 samples =
$3.40/sample
KAPA Biosystems Illumina Library Prep Kit (Roche.com #KK8301): $971
for 48*4 samples = $5.05/sample
KAPA Beads (#KK8001) $450.00 for 30 mL, ~200 ul per
sample = $3.00/sample
DreamTaq ReadyMix (ThermoFisher Item #FERK1081) $91.93 per 5000 ul =
$0.17 per reaction = $2.89 per sample across all PCR replicates
Illumina MiSeq v3 2x300 PE kit (Illumina.com #MS-102-3003) =$1674.00
only used 7% lane here = $117.18 for all samples N=300 = $0.40/sample