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Detailed information for vg0410565076:
| Variant ID: vg0410565076 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565076 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGAAAACCAAGAAGTGTACTTAATCCTTTCCATGTAAGTGTGTATTCCTTATGGAAAAATCAAAAGGAAATTCCATCTTCTATTTCTTTCAAAGTGCACA[G/C]
AAATTGCAAAGTAAGCAAAAGAGAACCAGGCTCATCTACCACAACAAATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCT
Reverse complement sequence
AGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATTTGTTGTGGTAGATGAGCCTGGTTCTCTTTTGCTTACTTTGCAATTT[C/G]
TGTGCACTTTGAAAGAAATAGAAGATGGAATTTCCTTTTGATTTTTCCATAAGGAATACACACTTACATGGAAAGGATTAAGTACACTTCTTGGTTTTCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.50% | 0.10% | 0.49% | 59.84% | NA |
| All Indica | 2759 | 8.60% | 0.00% | 0.76% | 90.65% | NA |
| All Japonica | 1512 | 98.60% | 0.50% | 0.13% | 0.79% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 5.20% | 0.00% | 1.34% | 93.45% | NA |
| Indica II | 465 | 25.80% | 0.00% | 0.65% | 73.55% | NA |
| Indica III | 913 | 2.80% | 0.00% | 0.22% | 96.93% | NA |
| Indica Intermediate | 786 | 7.60% | 0.00% | 1.02% | 91.35% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 97.20% | 1.40% | 0.40% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 0.00% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565076 | G -> C | LOC_Os04g19010.1 | missense_variant ; p.Leu83Val; MODERATE | nonsynonymous_codon ; L83V | Average:7.075; most accessible tissue: Callus, score: 15.368 | benign  |
1.2 |
TOLERATED | 0.09 |
| vg0410565076 | G -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:7.075; most accessible tissue: Callus, score: 15.368 | N | N | N | N |