| Variant ID: vg0334098592 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098592 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 345. )
GATTTTGATCAGCTTACGTCTAACCGTGTTCGGTGGACTCCCTACACTCAGCACGATGACAATGATCGTGCACCACTCGGTCTCATGAACCTTTGCATGC[G/A]
AGATATGCAACTCTGGAGGACTACTTGTCACCTCGTGATGGATATGCACGTCGAGCCACACAATGTCCATAGGGTTATGAAATAATTGGGCATGTATCAA
TTGATACATGCCCAATTATTTCATAACCCTATGGACATTGTGTGGCTCGACGTGCATATCCATCACGAGGTGACAAGTAGTCCTCCAGAGTTGCATATCT[C/T]
GCATGCAAAGGTTCATGAGACCGAGTGGTGCACGATCATTGTCATCGTGCTGAGTGTAGGGAGTCCACCGAACACGGTTAGACGTAAGCTGATCAAAATC
| 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% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.60% | 0.00% | 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 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098592 | G -> A | LOC_Os03g59910.1 | missense_variant ; p.Arg74Gln; MODERATE | N | Average:45.694; most accessible tissue: Zhenshan97 young leaf, score: 55.261 | N | N | N | N |
| vg0334098592 | G -> A | LOC_Os03g59894.1 | downstream_gene_variant ; 1925.0bp to feature; MODIFIER | N | Average:45.694; most accessible tissue: Zhenshan97 young leaf, score: 55.261 | N | N | N | N |
| vg0334098592 | G -> A | LOC_Os03g59920.1 | downstream_gene_variant ; 969.0bp to feature; MODIFIER | N | Average:45.694; most accessible tissue: Zhenshan97 young leaf, score: 55.261 | N | N | N | N |