Table 1 Quality Control assessment of 21 trait-SNPs contain in the 1K-RiCA assay. The QC parameters ‘Utility’, ‘False Positive Rate’ (FPR), ‘False Negative Rate’ (FNR) were estimated for each SNP and haplotypes when more than 1 SNP was associated with a trait
SNP ID | Chr. | MSU7 Pos. | Gene | Negative Allele | Positive Allele | Negative Trait | Positive Trait | Use as | SNP Utility | SNP FPR | SNP FNR | Haplotype Utility | Haplotype FPR | Haplotype FNR |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
chr03:16733441 | 3 | 16.73 | GS3 | G | T | Short | Long | Use as single SNP (T) | 34.8% | 0.0% | 0.0% | Â | Â | Â |
chr05:437499 | 5 | 0.44 | xa5 | T | A | Susceptible | Resistant | Use as single SNP (A) | 91.4% | 0.0% | 0.0% | Â | Â | Â |
chr06:27275515 | 6 | 27.28 | Xa7 | G | A | Susceptible | Resistant | Use haplotype (AAC) | Â | 96.2% | 0.0% | 0.0% | ||
chr06:27627615 | 6 | 27.63 | Xa7 | C | A | |||||||||
chr06:27761109 | 6 | 27.76 | Xa7 | A | C | |||||||||
chr08:26448560 | 8 | 26.45 | xa13 | T | G | Susceptible | Resistant | Use haplotype (GGC) | Â | 81.8% | 0.0% | 0.0% | ||
chr08:26709228 | 8 | 26.71 | xa13 | A | G | |||||||||
chr08:26898822 | 8 | 26.90 | xa13 | T | C | |||||||||
chr11:27603799 | 11 | 27.60 | Xa4 | C | A | Susceptible | Resistant | Use as single SNP (A) | 52.4% | 0.0% | 0.0% | Â | Â | Â |
chr11:21190115 | 11 | 21.19 | Xa21 | C | T | Susceptible | Resistant | Use as single SNP (T) | 98.4% | 0.0% | 0.0% | Â | Â | Â |
chr11:22162729 | 11 | 22.16 | Xa23 | C | T | Susceptible | Resistant | Use as haplotype (TTA) | Â | 96.5% | 0.0% | 0.0% | ||
chr11:22453819 | 11 | 22.45 | Xa23 | C | T | |||||||||
chr11:23231455 | 11 | 23.23 | Xa23 | G | A | |||||||||
chr07:22119347 | 7 | 22.12 | rstv | A | G | Susceptible | Resistant | Use as single SNP (G) | 91.9% | 0.0% | 80.0% | Â | Â | Â |
chr09:5922125 | 9 | 5.92 | sub1 | C | T | Susceptible | Tolerant | Use haplotype (TAG) | Â | 88.1% | 0.0% | 0.0% | ||
chr09:6252407 | 9 | 6.25 | sub1 | G | A | |||||||||
chr09:6913547 | 9 | 6.91 | sub1 | C | G | |||||||||
chr06:6752756 | 6 | 6.75 | ALK | A | G | Low-GT | High-GT | Use as single SNP | 98.8% | 0.0% | 60.0% | Â | Â | Â |
chr06:1765761 | 6 | 1.766 | Wxt/wx | G | T | Depends on market preference | Depends on market preference | Use haplotype to differentiate high (GAC/GAC), intermediate (GCC) and low (TAC/TCC) ACC | 84.3% | 0.0% | 0.0% | Â | ||
chr06:1768006 | 6 | 1.768 | Wxin (Wxg1) | A | C | 60.8% | 0.0% | 75.0% | ||||||
chr06:1768998 | 6 | 1.769 | Wxa (Wxg2) | C | T | 75.2% | 66.7% | 100.0% | ||||||