| Variant ID: vg0203137445 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 3137445 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )
ATTTGGAAGGAAGCTGGAATTTTTTTTCCCAATGTAATGAGTAGAGGGTATAGTCTGCCCAGTTTCAGGGTTTCTCCCCCTCCAGTCGGAGGCTGTGCCT[C/T]
GGACCATGCTCGACATGCTTTTGTCGATGTAACTATACTTTTGTACTTTGTTTTTTTTTTACTAATTCTTAATGAAATTGGTTGGCCACTCTTTGGCTGA
TCAGCCAAAGAGTGGCCAACCAATTTCATTAAGAATTAGTAAAAAAAAAACAAAGTACAAAAGTATAGTTACATCGACAAAAGCATGTCGAGCATGGTCC[G/A]
AGGCACAGCCTCCGACTGGAGGGGGAGAAACCCTGAAACTGGGCAGACTATACCCTCTACTCATTACATTGGGAAAAAAAATTCCAGCTTCCTTCCAAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.20% | 0.50% | 0.55% | 1.76% | NA |
| All Indica | 2759 | 97.70% | 0.00% | 0.47% | 1.85% | NA |
| All Japonica | 1512 | 97.70% | 1.50% | 0.66% | 0.20% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.00% | 0.37% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.30% | 0.00% | 0.44% | 3.29% | NA |
| Indica Intermediate | 786 | 96.30% | 0.00% | 1.02% | 2.67% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 4.40% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 2.08% | 26.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 1.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203137445 | C -> T | LOC_Os02g06270.1 | upstream_gene_variant ; 2460.0bp to feature; MODIFIER | silent_mutation | Average:63.052; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137445 | C -> T | LOC_Os02g06290.1 | upstream_gene_variant ; 4547.0bp to feature; MODIFIER | silent_mutation | Average:63.052; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137445 | C -> T | LOC_Os02g06290.2 | upstream_gene_variant ; 4849.0bp to feature; MODIFIER | silent_mutation | Average:63.052; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137445 | C -> T | LOC_Os02g06280.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.052; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137445 | C -> DEL | N | N | silent_mutation | Average:63.052; most accessible tissue: Callus, score: 83.704 | N | N | N | N |