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Detailed information for vg0206047353:
| Variant ID: vg0206047353 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6047353 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
AGGATTTGCAGCCGGGATCTTCGGTACTGGGGCCTCTTCGTCTCACGCCGGTAGGACTGGTCCTACTAGCCAGTTCTACGACGACGACTTGCACGGTGCA[C/T]
ACCACCACGACGTACTAGGCTCCTCTCAGCTTGGAGGAGCTCCAGAGGCGCACACTCAGGAGCAGCCAGAGGTCACACCTGTACAGGCAGGACGGGTTGG
Reverse complement sequence
CCAACCCGTCCTGCCTGTACAGGTGTGACCTCTGGCTGCTCCTGAGTGTGCGCCTCTGGAGCTCCTCCAAGCTGAGAGGAGCCTAGTACGTCGTGGTGGT[G/A]
TGCACCGTGCAAGTCGTCGTCGTAGAACTGGCTAGTAGGACCAGTCCTACCGGCGTGAGACGAAGAGGCCCCAGTACCGAAGATCCCGGCTGCAAATCCT
Allele Frequencies:
| 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 | 33.80% | 3.20% | 5.54% | 57.45% | NA |
| All Indica | 2759 | 1.60% | 1.30% | 5.00% | 92.17% | NA |
| All Japonica | 1512 | 97.80% | 0.00% | 0.13% | 2.05% | NA |
| Aus | 269 | 0.40% | 39.80% | 39.78% | 20.07% | NA |
| Indica I | 595 | 0.50% | 0.20% | 4.03% | 95.29% | NA |
| Indica II | 465 | 1.50% | 0.60% | 2.80% | 95.05% | NA |
| Indica III | 913 | 1.60% | 0.80% | 6.24% | 91.35% | NA |
| Indica Intermediate | 786 | 2.30% | 3.10% | 5.60% | 89.06% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.13% | 1.69% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.20% | 1.98% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.00% | 3.32% | NA |
| VI/Aromatic | 96 | 37.50% | 5.20% | 11.46% | 45.83% | NA |
| Intermediate | 90 | 44.40% | 3.30% | 4.44% | 47.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206047353 | C -> T | LOC_Os02g11730.1 | missense_variant ; p.His1512Tyr; MODERATE | nonsynonymous_codon ; H1512Y | Average:5.423; most accessible tissue: Minghui63 flower, score: 7.958 | possibly damaging  |
1.614 |
DELETERIOUS | 0.04 |
| vg0206047353 | C -> DEL | LOC_Os02g11730.1 | N | frameshift_variant | Average:5.423; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |