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Detailed information for vg0101920299:
| Variant ID: vg0101920299 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920299 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 390. )
Flanking Sequence (100 bp) in Reference Genome:
AGATTATACTCTGATCAGAGGTGTACATCTTTACCCACAAGACACATCTTCCTCACGTGTAACCACGTGCCACATACCACCACGGTATACAGACGGAAGA[C/T]
GTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCT
Reverse complement sequence
AGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCAC[G/A]
TCTTCCGTCTGTATACCGTGGTGGTATGTGGCACGTGGTTACACGTGAGGAAGATGTGTCTTGTGGGTAAAGATGTACACCTCTGATCAGAGTATAATCT
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 | 59.40% | 0.00% | 7.49% | 33.03% | NA |
| All Indica | 2759 | 48.40% | 0.10% | 11.45% | 40.09% | NA |
| All Japonica | 1512 | 71.90% | 0.00% | 1.46% | 26.65% | NA |
| Aus | 269 | 90.30% | 0.00% | 2.60% | 7.06% | NA |
| Indica I | 595 | 26.90% | 0.00% | 9.24% | 63.87% | NA |
| Indica II | 465 | 42.40% | 0.20% | 12.26% | 45.16% | NA |
| Indica III | 913 | 66.40% | 0.10% | 12.05% | 21.47% | NA |
| Indica Intermediate | 786 | 47.30% | 0.00% | 11.96% | 40.71% | NA |
| Temperate Japonica | 767 | 81.90% | 0.00% | 1.96% | 16.17% | NA |
| Tropical Japonica | 504 | 63.10% | 0.00% | 0.79% | 36.11% | NA |
| Japonica Intermediate | 241 | 58.50% | 0.00% | 1.24% | 40.25% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 2.08% | 7.29% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 7.78% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920299 | C -> T | LOC_Os01g04310.1 | missense_variant ; p.Val45Ile; MODERATE | nonsynonymous_codon ; V45I | Average:9.136; most accessible tissue: Callus, score: 15.504 | benign  |
0.877 |
TOLERATED | 0.09 |
| vg0101920299 | C -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:9.136; most accessible tissue: Callus, score: 15.504 | N | N | N | N |