| Variant ID: vg0903405748 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3405748 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, T: 0.24, others allele: 0.00, population size: 218. )
GTTTTGATATAACCTCTACTGATTTTTTAGGATTAAAACACAAATAAAGAAAAAACAAACTTTCCACAATACATCAATCAAAGAAACATATATGCGTATT[T/A]
CCACATATGAGTTCAATTCCAACAGAACTTTTGAAAGATATGTACTAACCATAGTCTGTGTGAGCTCCACTGAATTGATCGTAGAATGGATGCCATGTAA
TTACATGGCATCCATTCTACGATCAATTCAGTGGAGCTCACACAGACTATGGTTAGTACATATCTTTCAAAAGTTCTGTTGGAATTGAACTCATATGTGG[A/T]
AATACGCATATATGTTTCTTTGATTGATGTATTGTGGAAAGTTTGTTTTTTCTTTATTTGTGTTTTAATCCTAAAAAATCAGTAGAGGTTATATCAAAAC
| 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 | 63.90% | 36.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 50.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903405748 | T -> A | LOC_Os09g07010.1 | upstream_gene_variant ; 2639.0bp to feature; MODIFIER | silent_mutation | Average:49.33; most accessible tissue: Callus, score: 77.599 | N | N | N | N |
| vg0903405748 | T -> A | LOC_Os09g07030.1 | downstream_gene_variant ; 3132.0bp to feature; MODIFIER | silent_mutation | Average:49.33; most accessible tissue: Callus, score: 77.599 | N | N | N | N |
| vg0903405748 | T -> A | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.33; most accessible tissue: Callus, score: 77.599 | N | N | N | N |
| vg0903405748 | T -> A | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:49.33; most accessible tissue: Callus, score: 77.599 | N | N | N | N |