| Variant ID: vg1224818915 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 24818915 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 336. )
TCAATATCGTTTAAGAGTAATTCACAACATCACAATCTCAGAAGAACATTCTAAGGACACACTGCAAACTTGTGCTTACTTGGATTAGTCTTGGTCTTGC[C/T]
ATTCAATTTCTTTGAAGTAGAGGCCTTGTGAGGAGATCCAACTAGAAATGTTGATGGTGTGCTAGTATCTTCAGAATCACTTAAATGGTATTGCTCAGCA
TGCTGAGCAATACCATTTAAGTGATTCTGAAGATACTAGCACACCATCAACATTTCTAGTTGGATCTCCTCACAAGGCCTCTACTTCAAAGAAATTGAAT[G/A]
GCAAGACCAAGACTAATCCAAGTAAGCACAAGTTTGCAGTGTGTCCTTAGAATGTTCTTCTGAGATTGTGATGTTGTGAATTACTCTTAAACGATATTGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.30% | 6.60% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 96.10% | 3.80% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 88.60% | 11.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.10% | 3.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 74.20% | 25.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1224818915 | C -> T | LOC_Os12g40120.1 | missense_variant ; p.Gly178Ser; MODERATE | nonsynonymous_codon ; G178S | Average:47.348; most accessible tissue: Zhenshan97 young leaf, score: 66.32 | unknown | unknown | TOLERATED | 0.09 |