| Variant ID: vg1222999902 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999902 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.11, T: 0.02, others allele: 0.00, population size: 55. )
CAAACATAATCAAGACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTTCATATTATAA[A/G]
ACTTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATAT
ATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAAGT[T/C]
TTATAATATGAAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGTCTTGATTATGTTTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.10% | 7.30% | 19.30% | 47.25% | NA |
| All Indica | 2759 | 21.60% | 11.90% | 27.73% | 38.78% | NA |
| All Japonica | 1512 | 27.30% | 0.30% | 6.94% | 65.41% | NA |
| Aus | 269 | 66.20% | 1.90% | 8.18% | 23.79% | NA |
| Indica I | 595 | 12.80% | 2.00% | 23.53% | 61.68% | NA |
| Indica II | 465 | 40.60% | 1.90% | 20.65% | 36.77% | NA |
| Indica III | 913 | 13.60% | 26.90% | 33.63% | 25.85% | NA |
| Indica Intermediate | 786 | 26.20% | 7.90% | 28.24% | 37.66% | NA |
| Temperate Japonica | 767 | 23.30% | 0.00% | 2.35% | 74.32% | NA |
| Tropical Japonica | 504 | 30.00% | 1.00% | 14.29% | 54.76% | NA |
| Japonica Intermediate | 241 | 34.40% | 0.00% | 6.22% | 59.34% | NA |
| VI/Aromatic | 96 | 27.10% | 1.00% | 4.17% | 67.71% | NA |
| Intermediate | 90 | 25.60% | 6.70% | 17.78% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999902 | A -> DEL | N | N | silent_mutation | Average:29.592; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999902 | A -> G | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 356.0bp to feature; MODIFIER | silent_mutation | Average:29.592; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999902 | A -> G | LOC_Os12g37470.1 | upstream_gene_variant ; 1378.0bp to feature; MODIFIER | silent_mutation | Average:29.592; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999902 | A -> G | LOC_Os12g37490.1 | downstream_gene_variant ; 2309.0bp to feature; MODIFIER | silent_mutation | Average:29.592; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |