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Detailed information for vg0410079692:
| Variant ID: vg0410079692 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079692 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 120. )
Flanking Sequence (100 bp) in Reference Genome:
ACTCCAAGAGCTTTCCATCAAGTACTCACGGGCCGAAAACGGAGGTCGTATGCAGATTCGGCAGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCGAATC[G/A]
GATTCCAGCACTTGGAGGATTTGATCTTGATATCTTCTTGTTCATCCATGATGTGAGCAATGGTTGCATCTGTGGTAGCCATGGTCACATCATCCTCCCC
Reverse complement sequence
GGGGAGGATGATGTGACCATGGCTACCACAGATGCAACCATTGCTCACATCATGGATGAACAAGAAGATATCAAGATCAAATCCTCCAAGTGCTGGAATC[C/T]
GATTCGGCCACCTACTACACTGCTGACTTCAAACGGCTGCCGAATCTGCATACGACCTCCGTTTTCGGCCCGTGAGTACTTGATGGAAAGCTCTTGGAGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.90% | 4.60% | 11.89% | 62.57% | NA |
| All Indica | 2759 | 1.40% | 7.80% | 17.18% | 73.61% | NA |
| All Japonica | 1512 | 61.30% | 0.10% | 2.45% | 36.18% | NA |
| Aus | 269 | 1.10% | 0.00% | 13.38% | 85.50% | NA |
| Indica I | 595 | 0.70% | 12.40% | 18.66% | 68.24% | NA |
| Indica II | 465 | 1.70% | 12.90% | 16.34% | 69.03% | NA |
| Indica III | 913 | 1.40% | 1.50% | 17.42% | 79.63% | NA |
| Indica Intermediate | 786 | 1.70% | 8.70% | 16.28% | 73.41% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | NA |
| Tropical Japonica | 504 | 5.80% | 0.00% | 5.95% | 88.29% | NA |
| Japonica Intermediate | 241 | 67.60% | 0.40% | 2.49% | 29.46% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 22.20% | 2.20% | 16.67% | 58.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079692 | G -> DEL | LOC_Os04g18230.1 | N | frameshift_variant | Average:7.473; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0410079692 | G -> A | LOC_Os04g18230.1 | missense_variant ; p.Pro28Leu; MODERATE | nonsynonymous_codon ; P28L | Average:7.473; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
0.546 |
TOLERATED | 0.26 |