| Variant ID: vg1109585481 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9585481 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 404. )
CATTGCTAGCATCAGTAGCACCGAATTTAGTATTCAGTGCATCCCACAACTTCTTAGCGTCGGTCATATGCATATACACCTCGACCAGACGATCGCCAAG[A/G]
ACGCTAAGAATGCATCCCACAAAGAGAGTAGTGGCTTCCTCGAATTGCTTCTGCTGTTCAGCAGTAAGAACTCCTTCAGGTTTGCCAGTACTCACCCAGA
TCTGGGTGAGTACTGGCAAACCTGAAGGAGTTCTTACTGCTGAACAGCAGAAGCAATTCGAGGAAGCCACTACTCTCTTTGTGGGATGCATTCTTAGCGT[T/C]
CTTGGCGATCGTCTGGTCGAGGTGTATATGCATATGACCGACGCTAAGAAGTTGTGGGATGCACTGAATACTAAATTCGGTGCTACTGATGCTAGCAATG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.40% | 0.10% | 7.07% | 15.40% | NA |
| All Indica | 2759 | 97.10% | 0.00% | 1.99% | 0.94% | NA |
| All Japonica | 1512 | 40.30% | 0.50% | 13.76% | 45.50% | NA |
| Aus | 269 | 77.30% | 0.00% | 21.56% | 1.12% | NA |
| Indica I | 595 | 95.30% | 0.00% | 2.18% | 2.52% | NA |
| Indica II | 465 | 96.10% | 0.00% | 3.23% | 0.65% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 95.90% | 0.00% | 3.18% | 0.89% | NA |
| Temperate Japonica | 767 | 28.20% | 0.00% | 10.17% | 61.67% | NA |
| Tropical Japonica | 504 | 51.40% | 1.00% | 20.24% | 27.38% | NA |
| Japonica Intermediate | 241 | 55.60% | 0.80% | 11.62% | 31.95% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 6.25% | 5.21% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 7.78% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109585481 | A -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:6.757; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg1109585481 | A -> G | LOC_Os11g17200.1 | synonymous_variant ; p.Val68Val; LOW | synonymous_codon | Average:6.757; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |