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Detailed information for vg0410565096:
| Variant ID: vg0410565096 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565096 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, C: 0.32, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
TAATCCTTTCCATGTAAGTGTGTATTCCTTATGGAAAAATCAAAAGGAAATTCCATCTTCTATTTCTTTCAAAGTGCACAGAAATTGCAAAGTAAGCAAA[A/C]
GAGAACCAGGCTCATCTACCACAACAAATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTCCGG
Reverse complement sequence
CCGGAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATTTGTTGTGGTAGATGAGCCTGGTTCTC[T/G]
TTTGCTTACTTTGCAATTTCTGTGCACTTTGAAAGAAATAGAAGATGGAATTTCCTTTTGATTTTTCCATAAGGAATACACACTTACATGGAAAGGATTA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.80% | 17.70% | 6.24% | 52.26% | NA |
| All Indica | 2759 | 6.60% | 5.10% | 10.47% | 77.85% | NA |
| All Japonica | 1512 | 60.80% | 38.30% | 0.07% | 0.79% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.37% | 99.26% | NA |
| Indica I | 595 | 8.10% | 0.20% | 20.34% | 71.43% | NA |
| Indica II | 465 | 4.90% | 22.60% | 4.09% | 68.39% | NA |
| Indica III | 913 | 5.80% | 0.80% | 7.01% | 86.42% | NA |
| Indica Intermediate | 786 | 7.40% | 3.40% | 10.81% | 78.37% | NA |
| Temperate Japonica | 767 | 96.00% | 3.70% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 4.00% | 94.80% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 68.00% | 30.30% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 0.00% | 86.50% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 23.30% | 38.90% | 4.44% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565096 | A -> C | LOC_Os04g19010.1 | missense_variant ; p.Leu76Arg; MODERATE | nonsynonymous_codon ; L76R | Average:7.615; most accessible tissue: Callus, score: 15.368 | benign  |
-1.274 |
TOLERATED | 1.00 |
| vg0410565096 | A -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:7.615; most accessible tissue: Callus, score: 15.368 | N | N | N | N |