| Variant ID: vg0903405165 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3405165 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 331. )
AAATATGGACAGTGGGAAGAAACTGTAAGATGCTAATTGCATACTCCTAATTACTAATGCATCTTAGAAGATGCGTAGAATGTTAGAAAAGTAGAGAAGT[A/T]
TCTCTTGTTAGGTTATATGAGTCAAATTCTGTACAAAGATGCCCAGCTCAGATGCACTGCACTCTAATGAAAAATAAAACAATCTGAAATCAAGTTCTTA
TAAGAACTTGATTTCAGATTGTTTTATTTTTCATTAGAGTGCAGTGCATCTGAGCTGGGCATCTTTGTACAGAATTTGACTCATATAACCTAACAAGAGA[T/A]
ACTTCTCTACTTTTCTAACATTCTACGCATCTTCTAAGATGCATTAGTAATTAGGAGTATGCAATTAGCATCTTACAGTTTCTTCCCACTGTCCATATTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.50% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0903405165 | A -> T | LOC_Os09g07010.1 | upstream_gene_variant ; 2056.0bp to feature; MODIFIER | silent_mutation | Average:57.352; most accessible tissue: Zhenshan97 root, score: 77.733 | N | N | N | N |
| vg0903405165 | A -> T | LOC_Os09g07030.1 | downstream_gene_variant ; 3715.0bp to feature; MODIFIER | silent_mutation | Average:57.352; most accessible tissue: Zhenshan97 root, score: 77.733 | N | N | N | N |
| vg0903405165 | A -> T | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.352; most accessible tissue: Zhenshan97 root, score: 77.733 | N | N | N | N |
| vg0903405165 | A -> T | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:57.352; most accessible tissue: Zhenshan97 root, score: 77.733 | N | N | N | N |