| Variant ID: vg1225600169 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25600169 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )
ATCAGGCCTAGTTGCACTAGCCAGGTACATCAACGAGCCAATGATTTGGGAGTATTCCAGTTGATTCCTAGCAATTCTCTTGTTCTTGCGAAGCAACAAG[C/T]
TAGGATCATAAGGTGTTGGAGAAGGCTTACTATCAATATAGCCAAAACGATTCAAGATCTTCTCCACATAATGGGACTGCAAGAGTGTAATCCCATTCTC
GAGAATGGGATTACACTCTTGCAGTCCCATTATGTGGAGAAGATCTTGAATCGTTTTGGCTATATTGATAGTAAGCCTTCTCCAACACCTTATGATCCTA[G/A]
CTTGTTGCTTCGCAAGAACAAGAGAATTGCTAGGAATCAACTGGAATACTCCCAAATCATTGGCTCGTTGATGTACCTGGCTAGTGCAACTAGGCCTGAT
| 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 | 55.70% | 1.60% | 11.24% | 31.49% | NA |
| All Indica | 2759 | 35.60% | 2.70% | 18.34% | 43.35% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.07% | NA |
| Aus | 269 | 3.70% | 0.00% | 5.20% | 91.08% | NA |
| Indica I | 595 | 66.90% | 9.70% | 13.11% | 10.25% | NA |
| Indica II | 465 | 15.10% | 0.20% | 18.71% | 66.02% | NA |
| Indica III | 913 | 26.20% | 0.10% | 25.74% | 47.97% | NA |
| Indica Intermediate | 786 | 35.10% | 1.80% | 13.49% | 49.62% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 1.04% | 27.08% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 10.00% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225600169 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:10.529; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| vg1225600169 | C -> T | LOC_Os12g41280.1 | missense_variant ; p.Ser1065Asn; MODERATE | nonsynonymous_codon ; S1065N | Average:10.529; most accessible tissue: Zhenshan97 panicle, score: 28.447 | unknown | unknown | TOLERATED | 0.08 |