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Detailed information for vg0614257695:
| Variant ID: vg0614257695 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14257695 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 120. )
Flanking Sequence (100 bp) in Reference Genome:
TTCTTGACCTTCAAGTACAAACCCATCAGGTTGATCCATATAGATCTCCTCATCCAGCTCTCCATTAAGAAAAGCTGTCTTAACGTCCATTTGATGAATG[A/G]
GAAGACCATGTGAGGCTGCTAGGGAAAGTAGCACACGAATTGTGGTCAATCTAGCAACAGGTGAGTAAGTGTCAAAGAAATCTTCGCCTTCTTTCTGAGT
Reverse complement sequence
ACTCAGAAAGAAGGCGAAGATTTCTTTGACACTTACTCACCTGTTGCTAGATTGACCACAATTCGTGTGCTACTTTCCCTAGCAGCCTCACATGGTCTTC[T/C]
CATTCATCAAATGGACGTTAAGACAGCTTTTCTTAATGGAGAGCTGGATGAGGAGATCTATATGGATCAACCTGATGGGTTTGTACTTGAAGGTCAAGAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.70% | 11.50% | 6.75% | 62.10% | NA |
| All Indica | 2759 | 1.50% | 1.30% | 5.26% | 91.92% | NA |
| All Japonica | 1512 | 56.70% | 32.20% | 4.30% | 6.81% | NA |
| Aus | 269 | 1.90% | 0.70% | 32.71% | 64.68% | NA |
| Indica I | 595 | 2.70% | 0.20% | 7.23% | 89.92% | NA |
| Indica II | 465 | 0.60% | 1.30% | 4.95% | 93.12% | NA |
| Indica III | 913 | 1.10% | 0.50% | 4.05% | 94.30% | NA |
| Indica Intermediate | 786 | 1.70% | 3.10% | 5.34% | 89.95% | NA |
| Temperate Japonica | 767 | 92.70% | 2.90% | 1.04% | 3.39% | NA |
| Tropical Japonica | 504 | 7.90% | 71.80% | 8.13% | 12.10% | NA |
| Japonica Intermediate | 241 | 44.00% | 42.70% | 6.64% | 6.64% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 7.29% | 79.17% | NA |
| Intermediate | 90 | 14.40% | 18.90% | 15.56% | 51.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614257695 | A -> G | LOC_Os06g24360.1 | missense_variant ; p.Leu737Pro; MODERATE | nonsynonymous_codon ; L737P | Average:4.741; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | probably damaging  |
2.432 |
DELETERIOUS | 0.00 |
| vg0614257695 | A -> DEL | LOC_Os06g24360.1 | N | frameshift_variant | Average:4.741; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 | N | N | N | N |