Table 1.
Comparison of reference lines to published genome sequence
| Illumina 1536 SNP GoldenGate OPA | |||||
|---|---|---|---|---|---|
| ALCHEMY |
BeadStudio |
||||
| Line | #a | Agreementb | Call rate | Agreementb | Call rate |
| (%) | (%) | (%) | (%) | ||
| Nipponbare | 7 | 99.6 | 99.0 | 96.4 | 99.6 |
| 9311c | 7 | 95.6 | 98.0 | 93.3 | 98.4 |
| NPx9311 F1d | 6 | 93.6 | 96.7 | 91.7 | 99.8 |
| Average | 96.4 | 98.0 | 93.9 | 99.2 | |
| Affymetrix 44K GeneChip | |||||
| ALCHEMY |
BRLMM-P |
||||
| Line | #a | Agreementb | Call rate | Agreementb | Call rate |
| (%) | (%) | (%) | (%) | ||
| Nipponbare | 7 | 99.1 | 97.6 | 93.2 | 87.1 |
| 9311c | 5 | 96.5 | 96.4 | 89.1 | 87.1 |
| NPx9311 F1d | 6 | 94.7 | 92.7 | 90.3 | 84.5 |
| Average | 96.9 | 95.6 | 91.1 | 86.2 | |
aNumbers reported are averages across replicate samples.
bPercentage of genotype calls which agree with published sequence presuming homozygosity.
cThe 9311 line genotyped in this study was obtained from a different source than the sequenced line (see text).
dGenotypes predicted from parental genome sequence assuming normal Mendelian transmission and presuming homozygosity of the parents.