| Variant ID: vg0903405622 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3405622 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 268. )
TTATTCCTATAAGATATGTATTAGATGGTGAAGAAATAAGTACCTCAAGGGCGCATATGTCATCATCCTGATTAACCAATGTCAGAAGACCTACAAATTT[A/C]
ACAAATGATAAATATGATCCCCATGGTTTTGATATAACCTCTACTGATTTTTTAGGATTAAAACACAAATAAAGAAAAAACAAACTTTCCACAATACATC
GATGTATTGTGGAAAGTTTGTTTTTTCTTTATTTGTGTTTTAATCCTAAAAAATCAGTAGAGGTTATATCAAAACCATGGGGATCATATTTATCATTTGT[T/G]
AAATTTGTAGGTCTTCTGACATTGGTTAATCAGGATGATGACATATGCGCCCTTGAGGTACTTATTTCTTCACCATCTAATACATATCTTATAGGAATAA
| 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 | 99.30% | 0.60% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 71.90% | 25.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0903405622 | A -> C | LOC_Os09g07010.1 | upstream_gene_variant ; 2513.0bp to feature; MODIFIER | silent_mutation | Average:44.936; most accessible tissue: Zhenshan97 root, score: 65.566 | N | N | N | N |
| vg0903405622 | A -> C | LOC_Os09g07030.1 | downstream_gene_variant ; 3258.0bp to feature; MODIFIER | silent_mutation | Average:44.936; most accessible tissue: Zhenshan97 root, score: 65.566 | N | N | N | N |
| vg0903405622 | A -> C | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.936; most accessible tissue: Zhenshan97 root, score: 65.566 | N | N | N | N |
| vg0903405622 | A -> C | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:44.936; most accessible tissue: Zhenshan97 root, score: 65.566 | N | N | N | N |