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Detailed information for vg0409515286:
| Variant ID: vg0409515286 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515286 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
CCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTC[C/A]
ATACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCGTTCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAA
Reverse complement sequence
TTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGAACGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGTAT[G/T]
GAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.20% | 2.60% | 4.74% | 8.40% | NA |
| All Indica | 2759 | 89.30% | 3.60% | 7.07% | 0.00% | NA |
| All Japonica | 1512 | 73.70% | 0.50% | 0.86% | 24.93% | NA |
| Aus | 269 | 91.40% | 4.50% | 4.09% | 0.00% | NA |
| Indica I | 595 | 95.30% | 1.20% | 3.53% | 0.00% | NA |
| Indica II | 465 | 91.40% | 2.40% | 6.24% | 0.00% | NA |
| Indica III | 913 | 82.40% | 7.00% | 10.62% | 0.00% | NA |
| Indica Intermediate | 786 | 91.60% | 2.30% | 6.11% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 32.30% | 1.40% | 1.98% | 64.29% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 1.24% | 17.43% | NA |
| VI/Aromatic | 96 | 78.10% | 2.10% | 0.00% | 19.79% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 5.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515286 | C -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:29.234; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| vg0409515286 | C -> A | LOC_Os04g17380.1 | missense_variant ; p.Trp107Leu; MODERATE | nonsynonymous_codon ; W107L | Average:29.234; most accessible tissue: Minghui63 young leaf, score: 43.347 | possibly damaging  |
1.638 |
TOLERATED | 0.69 |