| Variant ID: vg0903405841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3405841 |
| 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, T: 0.00, others allele: 0.00, population size: 300. )
GCGTATTTCCACATATGAGTTCAATTCCAACAGAACTTTTGAAAGATATGTACTAACCATAGTCTGTGTGAGCTCCACTGAATTGATCGTAGAATGGATG[C/T]
CATGTAAAAGAAAAGCAGTGTCAGATGACTCTACACTCAATACACACGATTTGCAGGATATATTACCAAATAAAAACGTAGATACAATTTGCTCACCACC
GGTGGTGAGCAAATTGTATCTACGTTTTTATTTGGTAATATATCCTGCAAATCGTGTGTATTGAGTGTAGAGTCATCTGACACTGCTTTTCTTTTACATG[G/A]
CATCCATTCTACGATCAATTCAGTGGAGCTCACACAGACTATGGTTAGTACATATCTTTCAAAAGTTCTGTTGGAATTGAACTCATATGTGGAAATACGC
| 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 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 | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 80.20% | 19.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0903405841 | C -> T | LOC_Os09g07010.1 | upstream_gene_variant ; 2732.0bp to feature; MODIFIER | silent_mutation | Average:48.34; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |
| vg0903405841 | C -> T | LOC_Os09g07030.1 | downstream_gene_variant ; 3039.0bp to feature; MODIFIER | silent_mutation | Average:48.34; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |
| vg0903405841 | C -> T | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.34; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |
| vg0903405841 | C -> T | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.34; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |