| Variant ID: vg1109585537 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9585537 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 431. )
GCGTCGGTCATATGCATATACACCTCGACCAGACGATCGCCAAGAACGCTAAGAATGCATCCCACAAAGAGAGTAGTGGCTTCCTCGAATTGCTTCTGCT[G/A]
TTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGC
GCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAA[C/T]
AGCAGAAGCAATTCGAGGAAGCCACTACTCTCTTTGTGGGATGCATTCTTAGCGTTCTTGGCGATCGTCTGGTCGAGGTGTATATGCATATGACCGACGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.40% | 0.20% | 8.57% | 20.86% | NA |
| All Indica | 2759 | 94.60% | 0.30% | 3.55% | 1.49% | NA |
| All Japonica | 1512 | 24.10% | 0.00% | 14.81% | 61.04% | NA |
| Aus | 269 | 73.20% | 0.00% | 25.28% | 1.49% | NA |
| Indica I | 595 | 93.40% | 0.00% | 2.86% | 3.70% | NA |
| Indica II | 465 | 95.90% | 0.00% | 3.23% | 0.86% | NA |
| Indica III | 913 | 97.80% | 1.00% | 1.10% | 0.11% | NA |
| Indica Intermediate | 786 | 91.10% | 0.00% | 7.12% | 1.78% | NA |
| Temperate Japonica | 767 | 20.90% | 0.00% | 4.04% | 75.10% | NA |
| Tropical Japonica | 504 | 18.50% | 0.00% | 35.12% | 46.43% | NA |
| Japonica Intermediate | 241 | 46.50% | 0.00% | 6.64% | 46.89% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 7.29% | 8.33% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 8.89% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109585537 | G -> A | LOC_Os11g17200.1 | stop_gained ; p.Gln50*; HIGH | stop_gained | Average:7.459; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg1109585537 | G -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:7.459; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |