| Variant ID: vg1222498491 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22498491 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, C: 0.32, others allele: 0.00, population size: 54. )
CATCTCAATATAACAATTCTCTTACGTAACGATATAGGGGGAGGGGAAAAAAGGAATGTATAACTAGGAGTAAGAAGTTGATTGCACGCTGATATGCTAA[A/C]
GTTCATAAAGAGTTTTTTGGGTTTTTTTTAAGATAATGAATAACCTGGCAGCTGCATCAAAGACGTACATAGGCTATCATGCATTACTGTACGCCAAGCA
TGCTTGGCGTACAGTAATGCATGATAGCCTATGTACGTCTTTGATGCAGCTGCCAGGTTATTCATTATCTTAAAAAAAACCCAAAAAACTCTTTATGAAC[T/G]
TTAGCATATCAGCGTGCAATCAACTTCTTACTCCTAGTTATACATTCCTTTTTTCCCCTCCCCCTATATCGTTACGTAAGAGAATTGTTATATTGAGATG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.10% | 25.30% | 7.96% | 15.57% | NA |
| All Indica | 2759 | 24.90% | 40.60% | 13.16% | 21.28% | NA |
| All Japonica | 1512 | 91.70% | 3.00% | 0.46% | 4.83% | NA |
| Aus | 269 | 69.50% | 6.70% | 0.37% | 23.42% | NA |
| Indica I | 595 | 41.20% | 33.30% | 6.89% | 18.66% | NA |
| Indica II | 465 | 15.90% | 52.30% | 20.86% | 10.97% | NA |
| Indica III | 913 | 20.80% | 33.50% | 14.24% | 31.43% | NA |
| Indica Intermediate | 786 | 22.80% | 47.60% | 12.09% | 17.56% | NA |
| Temperate Japonica | 767 | 94.90% | 3.40% | 0.39% | 1.30% | NA |
| Tropical Japonica | 504 | 95.60% | 0.80% | 0.00% | 3.57% | NA |
| Japonica Intermediate | 241 | 73.00% | 6.60% | 1.66% | 18.67% | NA |
| VI/Aromatic | 96 | 88.50% | 3.10% | 2.08% | 6.25% | NA |
| Intermediate | 90 | 78.90% | 10.00% | 3.33% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222498491 | A -> C | LOC_Os12g36730.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.749; most accessible tissue: Minghui63 root, score: 64.607 | N | N | N | N |
| vg1222498491 | A -> DEL | N | N | silent_mutation | Average:40.749; most accessible tissue: Minghui63 root, score: 64.607 | N | N | N | N |