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Detailed information for vg0409515266:
| Variant ID: vg0409515266 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515266 |
| 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: 291. )
Flanking Sequence (100 bp) in Reference Genome:
AGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTC[C/T]
AATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCGTTCCTTATCTCTGGTA
Reverse complement sequence
TACCAGAGATAAGGAACGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATT[G/A]
GAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCT
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 | 83.80% | 2.10% | 5.65% | 8.40% | NA |
| All Indica | 2759 | 88.60% | 2.80% | 8.59% | 0.00% | NA |
| All Japonica | 1512 | 73.80% | 0.50% | 0.79% | 24.93% | NA |
| Aus | 269 | 91.10% | 4.10% | 4.83% | 0.00% | NA |
| Indica I | 595 | 95.00% | 1.30% | 3.70% | 0.00% | NA |
| Indica II | 465 | 91.60% | 1.10% | 7.31% | 0.00% | NA |
| Indica III | 913 | 80.70% | 5.50% | 13.80% | 0.00% | NA |
| Indica Intermediate | 786 | 91.10% | 1.90% | 7.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 32.50% | 1.40% | 1.79% | 64.29% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 1.24% | 17.43% | NA |
| VI/Aromatic | 96 | 77.10% | 2.10% | 1.04% | 19.79% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 4.44% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515266 | C -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:31.343; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
| vg0409515266 | C -> T | LOC_Os04g17380.1 | missense_variant ; p.Gly114Arg; MODERATE | nonsynonymous_codon ; G114R | Average:31.343; most accessible tissue: Minghui63 young leaf, score: 49.581 | benign  |
0.892 |
DELETERIOUS | 0.03 |