| Variant ID: vg0234310559 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34310559 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.01, others allele: 0.00, population size: 331. )
CTTGACCTGCAGGAGTTTGTGTAACCGTTTATGGCCTTTCAGGGAGATTGAAACAGAGGATTCTGATGGTTGCTGTTTAGGAAATTGAGTCGATGGACAT[A/T]
ATGAACTGACTTACGATCCTGGTATGAGAGGACAGTGCATCGAAGTGTAGCATTCTTCCACAGAGAGGTTTACCAACAGCAGTTGCAACCTTTATAGCCT
AGGCTATAAAGGTTGCAACTGCTGTTGGTAAACCTCTCTGTGGAAGAATGCTACACTTCGATGCACTGTCCTCTCATACCAGGATCGTAAGTCAGTTCAT[T/A]
ATGTCCATCGACTCAATTTCCTAAACAGCAACCATCAGAATCCTCTGTTTCAATCTCCCTGAAAGGCCATAAACGGTTACACAAACTCCTGCAGGTCAAG
| 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 | 97.50% | 2.50% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 64.70% | 35.30% | 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 | 99.20% | 0.70% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 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 | 93.80% | 6.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0234310559 | A -> T | LOC_Os02g56040.1 | upstream_gene_variant ; 2830.0bp to feature; MODIFIER | silent_mutation | Average:51.458; most accessible tissue: Callus, score: 80.669 | N | N | N | N |
| vg0234310559 | A -> T | LOC_Os02g56060.1 | upstream_gene_variant ; 2147.0bp to feature; MODIFIER | silent_mutation | Average:51.458; most accessible tissue: Callus, score: 80.669 | N | N | N | N |
| vg0234310559 | A -> T | LOC_Os02g56050.1 | intron_variant ; MODIFIER | silent_mutation | Average:51.458; most accessible tissue: Callus, score: 80.669 | N | N | N | N |