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Detailed information for vg0100790495:
| Variant ID: vg0100790495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 790495 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.35, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
CTCAAACTTAAAAGAAAAGGCAAATAAAGTCATCAACTTTGGTGAAACAGCATTTACTTGGCACCTTAACAAGATTACCAATGCTTGTCAGGGGTGTGAG[T/C]
GGAATGGTCATCACTGCGGATTTAGTTCACAAAGGGGCCAGGCATTCTGCCAGCATCAAGGTATCCTTCATCTCATATTTTTTTTTCACAAGGGAATTCT
Reverse complement sequence
AGAATTCCCTTGTGAAAAAAAAATATGAGATGAAGGATACCTTGATGCTGGCAGAATGCCTGGCCCCTTTGTGAACTAAATCCGCAGTGATGACCATTCC[A/G]
CTCACACCCCTGACAAGCATTGGTAATCTTGTTAAGGTGCCAAGTAAATGCTGTTTCACCAAAGTTGATGACTTTATTTGCCTTTTCTTTTAAGTTTGAG
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 | 39.70% | 15.80% | 1.21% | 43.31% | NA |
| All Indica | 2759 | 46.50% | 2.70% | 1.56% | 49.26% | NA |
| All Japonica | 1512 | 29.30% | 43.30% | 0.46% | 26.92% | NA |
| Aus | 269 | 34.20% | 1.10% | 0.37% | 64.31% | NA |
| Indica I | 595 | 68.10% | 0.70% | 0.00% | 31.26% | NA |
| Indica II | 465 | 73.10% | 1.90% | 1.08% | 23.87% | NA |
| Indica III | 913 | 16.60% | 0.80% | 1.75% | 80.83% | NA |
| Indica Intermediate | 786 | 49.00% | 7.00% | 2.80% | 41.22% | NA |
| Temperate Japonica | 767 | 2.90% | 67.00% | 0.39% | 29.73% | NA |
| Tropical Japonica | 504 | 77.60% | 5.40% | 0.40% | 16.67% | NA |
| Japonica Intermediate | 241 | 12.40% | 47.30% | 0.83% | 39.42% | NA |
| VI/Aromatic | 96 | 9.40% | 1.00% | 2.08% | 87.50% | NA |
| Intermediate | 90 | 53.30% | 15.60% | 4.44% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100790495 | T -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:45.082; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790495 | T -> C | LOC_Os01g02440.1 | missense_variant ; p.Trp177Arg; MODERATE | nonsynonymous_codon ; W177R | Average:45.082; most accessible tissue: Callus, score: 77.623 | probably damaging  |
-2.481 |
TOLERATED | 0.69 |