| Variant ID: vg0725375360 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25375360 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 304. )
AGATTATTTATGTGATCAATTTATCATGCAGGTGACTTGAATCTAAACATTATTCCTTCTGCACGGTGCCTGCTCCACGATACTGGCGTTGAAGCAGTGA[G/A]
AACAGGCCATGCGGAGCTCCCCCGAATAAAAGTTTCCAACTTGTAAATTATGCAGCTGTAGGAAATCCCAGCTATTGAGGCGCCCATCCTACTTAGGCTC
GAGCCTAAGTAGGATGGGCGCCTCAATAGCTGGGATTTCCTACAGCTGCATAATTTACAAGTTGGAAACTTTTATTCGGGGGAGCTCCGCATGGCCTGTT[C/T]
TCACTGCTTCAACGCCAGTATCGTGGAGCAGGCACCGTGCAGAAGGAATAATGTTTAGATTCAAGTCACCTGCATGATAAATTGATCACATAAATAATCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.60% | 0.04% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.80% | 0.11% | 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 | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725375360 | G -> A | LOC_Os07g42400.1 | missense_variant ; p.Arg728Lys; MODERATE | N | Average:68.075; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |
| vg0725375360 | G -> A | LOC_Os07g42400.2 | 3_prime_UTR_variant ; 397.0bp to feature; MODIFIER | N | Average:68.075; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |
| vg0725375360 | G -> A | LOC_Os07g42395.1 | upstream_gene_variant ; 3553.0bp to feature; MODIFIER | N | Average:68.075; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |
| vg0725375360 | G -> A | LOC_Os07g42395.2 | upstream_gene_variant ; 3504.0bp to feature; MODIFIER | N | Average:68.075; most accessible tissue: Zhenshan97 flower, score: 83.812 | N | N | N | N |