| Variant ID: vg0727004290 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27004290 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 381. )
TGCCATTTGACAAACCAACTTGGATCCCTGACAAAAAGCTGGAGTGTGGTCTTTCTGTTTTTAGAACATCAGATCGCGTGCAGTCTGTCATGGATGAGGA[A/T]
GAGCAACAGAGTAGCAGCACTTAGAGTAGATCAGTTTCAGACAATTCAGGGCAGCAAAAAGCACCTAGAAGAACCTAGTCAAGCTTGAACCTGTGTTATT
AATAACACAGGTTCAAGCTTGACTAGGTTCTTCTAGGTGCTTTTTGCTGCCCTGAATTGTCTGAAACTGATCTACTCTAAGTGCTGCTACTCTGTTGCTC[T/A]
TCCTCATCCATGACAGACTGCACGCGATCTGATGTTCTAAAAACAGAAAGACCACACTCCAGCTTTTTGTCAGGGATCCAAGTTGGTTTGTCAAATGGCA
| 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 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.30% | 0.13% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.00% | 0.40% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727004290 | A -> T | LOC_Os07g45250.1 | missense_variant ; p.Glu742Asp; MODERATE | N | Average:54.675; most accessible tissue: Callus, score: 90.008 | N | N | N | N |
| vg0727004290 | A -> T | LOC_Os07g45194.1 | upstream_gene_variant ; 3264.0bp to feature; MODIFIER | N | Average:54.675; most accessible tissue: Callus, score: 90.008 | N | N | N | N |
| vg0727004290 | A -> T | LOC_Os07g45260.1 | upstream_gene_variant ; 2333.0bp to feature; MODIFIER | N | Average:54.675; most accessible tissue: Callus, score: 90.008 | N | N | N | N |