| Variant ID: vg1222999916 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999916 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 86. )
ACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTTCATATTATAAAACTTTGTAACATT[A/G]
TCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATATATATATATATACAT
ATGTATATATATATATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGA[T/C]
AATGTTACAAAGTTTTATAATATGAAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.20% | 0.90% | 25.29% | 60.60% | NA |
| All Indica | 2759 | 19.50% | 0.10% | 25.77% | 54.66% | NA |
| All Japonica | 1512 | 3.60% | 2.60% | 24.21% | 69.64% | NA |
| Aus | 269 | 7.10% | 0.00% | 31.60% | 61.34% | NA |
| Indica I | 595 | 10.10% | 0.20% | 11.09% | 78.66% | NA |
| Indica II | 465 | 4.50% | 0.20% | 45.38% | 49.89% | NA |
| Indica III | 913 | 33.00% | 0.00% | 24.53% | 42.50% | NA |
| Indica Intermediate | 786 | 19.80% | 0.00% | 26.72% | 53.44% | NA |
| Temperate Japonica | 767 | 2.50% | 4.20% | 16.43% | 76.92% | NA |
| Tropical Japonica | 504 | 3.20% | 0.80% | 35.91% | 60.12% | NA |
| Japonica Intermediate | 241 | 7.90% | 1.20% | 24.48% | 66.39% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 17.71% | 78.12% | NA |
| Intermediate | 90 | 11.10% | 1.10% | 17.78% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999916 | A -> DEL | N | N | silent_mutation | Average:29.563; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg1222999916 | A -> G | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 342.0bp to feature; MODIFIER | silent_mutation | Average:29.563; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg1222999916 | A -> G | LOC_Os12g37470.1 | upstream_gene_variant ; 1392.0bp to feature; MODIFIER | silent_mutation | Average:29.563; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg1222999916 | A -> G | LOC_Os12g37490.1 | downstream_gene_variant ; 2295.0bp to feature; MODIFIER | silent_mutation | Average:29.563; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |