| Variant ID: vg0114526716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526716 |
| Reference Allele: T | Alternative Allele: C |
| 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: 268. )
GCAGGAATAGTTCTGCAAATAAGAAACACATGATCAAAACTAGAAAAGAAGCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTGAAGA[T/C]
TCACCAAATCGAGAATATGGCATCTCTACCAAATCGACAATATAGCATCTCCAAGGCTTCGAGATAGTACTAGATAATAAATCTGCTTTCCAGGTCGTGT
ACACGACCTGGAAAGCAGATTTATTATCTAGTACTATCTCGAAGCCTTGGAGATGCTATATTGTCGATTTGGTAGAGATGCCATATTCTCGATTTGGTGA[A/G]
TCTTCAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGCTTCTTTTCTAGTTTTGATCATGTGTTTCTTATTTGCAGAACTATTCCTGC
| 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 | 61.90% | 33.70% | 0.04% | 4.40% | NA |
| All Indica | 2759 | 90.90% | 1.60% | 0.07% | 7.39% | NA |
| All Japonica | 1512 | 2.60% | 97.30% | 0.00% | 0.07% | NA |
| Aus | 269 | 98.90% | 0.40% | 0.00% | 0.74% | NA |
| Indica I | 595 | 93.90% | 0.70% | 0.17% | 5.21% | NA |
| Indica II | 465 | 93.80% | 3.00% | 0.22% | 3.01% | NA |
| Indica III | 913 | 90.60% | 0.80% | 0.00% | 8.65% | NA |
| Indica Intermediate | 786 | 87.30% | 2.50% | 0.00% | 10.18% | NA |
| Temperate Japonica | 767 | 1.20% | 98.70% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 5.20% | 94.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 67.70% | 32.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 48.90% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526716 | T -> DEL | N | N | silent_mutation | Average:49.29; most accessible tissue: Zhenshan97 flower, score: 76.539 | N | N | N | N |
| vg0114526716 | T -> C | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.29; most accessible tissue: Zhenshan97 flower, score: 76.539 | N | N | N | N |