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Detailed information for vg0318603416:
| Variant ID: vg0318603416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18603416 |
| 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: 363. )
Flanking Sequence (100 bp) in Reference Genome:
TCCTATGCTTTGAACAAAAGGAAAAGGTGGCAGCAATCAAACCTGGAAATAGCGACCCCGCTCTTTTGCACTCTCAACAAGGTTGTTCCAGTGTTTATCT[T/C]
CCTTCAATGTTGAAGCAGAACCTACAACCTGTGGTATGACAAGTATTATTTGGATTGATAACTAAACCAACAAAGTTAACTACATAAGCAAATAGTGATA
Reverse complement sequence
TATCACTATTTGCTTATGTAGTTAACTTTGTTGGTTTAGTTATCAATCCAAATAATACTTGTCATACCACAGGTTGTAGGTTCTGCTTCAACATTGAAGG[A/G]
AGATAAACACTGGAACAACCTTGTTGAGAGTGCAAAAGAGCGGGGTCGCTATTTCCAGGTTTGATTGCTGCCACCTTTTCCTTTTGTTCAAAGCATAGGA
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 | 97.20% | 0.10% | 0.53% | 2.22% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 91.60% | 0.00% | 1.52% | 6.88% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 3.77% | 18.06% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 1.66% | 5.39% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0318603416 | T -> C | LOC_Os03g32526.1 | missense_variant ; p.Glu738Gly; MODERATE | nonsynonymous_codon ; E738G | Average:7.885; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.09 |
TOLERATED | 0.12 |
| vg0318603416 | T -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:7.885; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |