| Variant ID: vg0722037158 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 22037158 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 304. )
TACAGAACTACAGAAAAGCATAGCATATGTACAACATGAGTCACTCATATTACTCTCAAATACGTAAATGTCTTTCCCTAATCAAATTCAGGATTTTCTG[A/G]
TTTATGTGCTCTGAAATTGTGAACCACCTGAAGTAGAACTCTTTGTCTGCGAAGAAGCTGTGCTATTATGCATCTGCGAAGTTTGACTTGATGAAACATC
GATGTTTCATCAAGTCAAACTTCGCAGATGCATAATAGCACAGCTTCTTCGCAGACAAAGAGTTCTACTTCAGGTGGTTCACAATTTCAGAGCACATAAA[T/C]
CAGAAAATCCTGAATTTGATTAGGGAAAGACATTTACGTATTTGAGAGTAATATGAGTGACTCATGTTGTACATATGCTATGCTTTTCTGTAGTTCTGTA
| 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 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.60% | 11.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.50% | 6.50% | 0.00% | 0.00% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0722037158 | A -> G | LOC_Os07g36780.1 | 3_prime_UTR_variant ; 2.0bp to feature; MODIFIER | silent_mutation | Average:51.896; most accessible tissue: Callus, score: 67.457 | N | N | N | N |
| vg0722037158 | A -> G | LOC_Os07g36770.1 | upstream_gene_variant ; 2298.0bp to feature; MODIFIER | silent_mutation | Average:51.896; most accessible tissue: Callus, score: 67.457 | N | N | N | N |