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Detailed information for vg0233334140:
| Variant ID: vg0233334140 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33334140 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 109. )
Flanking Sequence (100 bp) in Reference Genome:
CCCTTGGGATCAAGGATTTCTTCGTTGATGAATCCCATGAGTTGTTCTTGAACCGCCGCGATAAATTCCTTGTGTGTGGTCAGGTTATCCCTCATGAGAA[T/C]
AAACTATATGAATGTATGAAATTGATTAGTAATTAAACAAGAAATCGCTACGTAATGAAATTTTGAATTTATTTGTACGTACATCGAGCTCTCTTGTGGT
Reverse complement sequence
ACCACAAGAGAGCTCGATGTACGTACAAATAAATTCAAAATTTCATTACGTAGCGATTTCTTGTTTAATTACTAATCAATTTCATACATTCATATAGTTT[A/G]
TTCTCATGAGGGATAACCTGACCACACACAAGGAATTTATCGCGGCGGTTCAAGAACAACTCATGGGATTCATCAACGAAGAAATCCTTGATCCCAAGGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.90% | 0.20% | 0.66% | 63.20% | NA |
| All Indica | 2759 | 2.10% | 0.00% | 0.62% | 97.25% | NA |
| All Japonica | 1512 | 98.60% | 0.60% | 0.00% | 0.79% | NA |
| Aus | 269 | 3.00% | 0.00% | 4.09% | 92.94% | NA |
| Indica I | 595 | 1.00% | 0.00% | 0.67% | 98.32% | NA |
| Indica II | 465 | 3.00% | 0.00% | 0.65% | 96.34% | NA |
| Indica III | 913 | 0.90% | 0.10% | 0.99% | 98.03% | NA |
| Indica Intermediate | 786 | 3.80% | 0.00% | 0.13% | 96.06% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0233334140 | T -> DEL | LOC_Os02g54400.1 | N | frameshift_variant | Average:5.739; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0233334140 | T -> C | LOC_Os02g54400.1 | missense_variant ; p.Ile893Val; MODERATE | nonsynonymous_codon ; I893V | Average:5.739; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
0.868 |
DELETERIOUS | 0.00 |