| Variant ID: vg1100672596 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 672596 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.72, A: 0.27, others allele: 0.00, population size: 263. )
CAAGGCTTTTCAGGGAAATGCCACAGAGGGATGTTGTTTCATTGAACTCTTTGATAAGTGGCTACACAAAGCTCGGCAAATATACCAAAGCATTGGAGAT[T/A]
TTTCAAGAAATGAAGGAGAATGCCATTGAACCTACGGAGCTTACACTTGTATTAATCCTTGGGGCTTGTGCAAAGGATGGCAAGCTGGAGCTGGGGACAG
CTGTCCCCAGCTCCAGCTTGCCATCCTTTGCACAAGCCCCAAGGATTAATACAAGTGTAAGCTCCGTAGGTTCAATGGCATTCTCCTTCATTTCTTGAAA[A/T]
ATCTCCAATGCTTTGGTATATTTGCCGAGCTTTGTGTAGCCACTTATCAAAGAGTTCAATGAAACAACATCCCTCTGTGGCATTTCCCTGAAAAGCCTTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.60% | 27.10% | 0.17% | 0.21% | NA |
| All Indica | 2759 | 59.60% | 39.80% | 0.25% | 0.36% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 39.80% | 59.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 64.00% | 35.30% | 0.67% | 0.00% | NA |
| Indica II | 465 | 76.30% | 23.00% | 0.00% | 0.65% | NA |
| Indica III | 913 | 47.90% | 51.70% | 0.00% | 0.44% | NA |
| Indica Intermediate | 786 | 59.80% | 39.40% | 0.38% | 0.38% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1100672596 | T -> A | LOC_Os11g02310.1 | synonymous_variant ; p.Ile131Ile; LOW | synonymous_codon | Average:76.55; most accessible tissue: Minghui63 flower, score: 84.49 | N | N | N | N |
| vg1100672596 | T -> DEL | LOC_Os11g02310.1 | N | frameshift_variant | Average:76.55; most accessible tissue: Minghui63 flower, score: 84.49 | N | N | N | N |