| Variant ID: vg0108457639 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457639 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: Unkown |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )
CTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGTC[G/A]
ACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGGTGAATAAAAGCAATACCGGCT
AGCCGGTATTGCTTTTATTCACCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGT[C/T]
GACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.20% | 0.00% | 5.18% | 0.57% | NA |
| All Indica | 2759 | 97.10% | 0.00% | 2.79% | 0.07% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.07% | NA |
| Aus | 269 | 29.70% | 0.00% | 61.34% | 8.92% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 0.00% | 1.29% | 0.00% | NA |
| Indica III | 913 | 96.30% | 0.00% | 3.72% | 0.00% | NA |
| Indica Intermediate | 786 | 95.00% | 0.00% | 4.71% | 0.25% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457639 | G -> A | LOC_Os01g15070.1 | missense_variant ; p.Asp72Asn; MODERATE | N | Average:52.565; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg0108457639 | G -> A | LOC_Os01g15080.1 | upstream_gene_variant ; 320.0bp to feature; MODIFIER | N | Average:52.565; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg0108457639 | G -> A | LOC_Os01g15090.1 | upstream_gene_variant ; 3433.0bp to feature; MODIFIER | N | Average:52.565; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg0108457639 | G -> A | LOC_Os01g15060.1 | downstream_gene_variant ; 1617.0bp to feature; MODIFIER | N | Average:52.565; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |