| Variant ID: vg0903742469 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3742469 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )
ACTGGTTCACGTGGTGGAACAGGAGCTCGCGGTTCATCTCCAAAACGAATCTCGCCCTCTTCGTGTATGTCCTCGACGACTCTTTCGATCACATTCACTT[C/A,T]
GCATGGGGAGTTGGATCCTGAAGATTCCTGGTCATCTAAGTTGTGAAGGACGGAAGGATCGATGTCGATGAATCCGACCAGGCGATCTGCAGTTCCCATT
AATGGGAACTGCAGATCGCCTGGTCGGATTCATCGACATCGATCCTTCCGTCCTTCACAACTTAGATGACCAGGAATCTTCAGGATCCAACTCCCCATGC[G/T,A]
AAGTGAATGTGATCGAAAGAGTCGTCGAGGACATACACGAAGAGGGCGAGATTCGTTTTGGAGATGAACCGCGAGCTCCTGTTCCACCACGTGAACCAGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.80% | 0.00% | 0.00% | T: 0.13% |
| All Indica | 2759 | 98.40% | 1.40% | 0.00% | 0.00% | T: 0.18% |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.00% | T: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.50% | 0.00% | 0.00% | T: 0.67% |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.70% | 0.00% | 0.00% | T: 0.13% |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.00% | T: 0.20% |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0903742469 | C -> T | LOC_Os09g07470.1 | missense_variant ; p.Glu57Lys; MODERATE | nonsynonymous_codon ; E57K | Average:67.34; most accessible tissue: Zhenshan97 young leaf, score: 82.982 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0903742469 | C -> A | LOC_Os09g07470.1 | stop_gained ; p.Glu57*; HIGH | stop_gained | Average:67.34; most accessible tissue: Zhenshan97 young leaf, score: 82.982 | N | N | N | N |