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Detailed information for vg0625223164:
| Variant ID: vg0625223164 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25223164 |
| 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: 400. )
Flanking Sequence (100 bp) in Reference Genome:
TGGGCACTCAGCGTTGTGTAAGATCCTGAGATCCCGAACCCATATATCTCCTCACTCCATGTATGAAAGATTGCTTCTTTCCTGAAATAATTTGAGACGT[A/G]
CACATTGGGAGATATGCCACAATCACCGGCAGCAGCAAGAACGTGTGAGCAAGGAAGGTGATGAAGCTTCGGCTTCATACAACTGCAGGTACATCCACCA
Reverse complement sequence
TGGTGGATGTACCTGCAGTTGTATGAAGCCGAAGCTTCATCACCTTCCTTGCTCACACGTTCTTGCTGCTGCCGGTGATTGTGGCATATCTCCCAATGTG[T/C]
ACGTCTCAAATTATTTCAGGAAAGAAGCAATCTTTCATACATGGAGTGAGGAGATATATGGGTTCGGGATCTCAGGATCTTACACAACGCTGAGTGCCCA
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 | 15.60% | 0.80% | 4.76% | 78.88% | NA |
| All Indica | 2759 | 0.80% | 0.40% | 4.93% | 93.91% | NA |
| All Japonica | 1512 | 46.20% | 0.30% | 0.79% | 52.65% | NA |
| Aus | 269 | 1.90% | 0.00% | 20.45% | 77.70% | NA |
| Indica I | 595 | 0.30% | 0.00% | 1.85% | 97.82% | NA |
| Indica II | 465 | 1.50% | 0.00% | 6.24% | 92.26% | NA |
| Indica III | 913 | 0.20% | 0.50% | 6.35% | 92.88% | NA |
| Indica Intermediate | 786 | 1.40% | 0.60% | 4.83% | 93.13% | NA |
| Temperate Japonica | 767 | 72.90% | 0.00% | 0.52% | 26.60% | NA |
| Tropical Japonica | 504 | 8.70% | 0.20% | 0.79% | 90.28% | NA |
| Japonica Intermediate | 241 | 39.80% | 1.70% | 1.66% | 56.85% | NA |
| VI/Aromatic | 96 | 1.00% | 22.90% | 16.67% | 59.38% | NA |
| Intermediate | 90 | 8.90% | 1.10% | 6.67% | 83.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625223164 | A -> G | LOC_Os06g42010.1 | missense_variant ; p.Tyr662His; MODERATE | nonsynonymous_codon ; Y662H | Average:4.679; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.025 |
DELETERIOUS | 0.03 |
| vg0625223164 | A -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.679; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |