Search for Variation information by Variation ID:
Detailed information for vg0136519596:
| Variant ID: vg0136519596 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36519596 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
AGAGAAGTGTGATTCCAAGAATTTTATTAAATTTTTACCGCCATCAATGGCTCTAGATGGGATCTTCGAACCGGAGCATAAGTTTAGGGGAGATAGCTCT[G/A]
GCACATGGGGGTTGTTTTCTCTTGGTTCCTTCATCAACTGAACAGCATGTATATCGGAAATTAGCTAAATTTTGCAGCCAGAAATAGGCATATTACAGCC
Reverse complement sequence
GGCTGTAATATGCCTATTTCTGGCTGCAAAATTTAGCTAATTTCCGATATACATGCTGTTCAGTTGATGAAGGAACCAAGAGAAAACAACCCCCATGTGC[C/T]
AGAGCTATCTCCCCTAAACTTATGCTCCGGTTCGAAGATCCCATCTAGAGCCATTGATGGCGGTAAAAATTTAATAAAATTCTTGGAATCACACTTCTCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.80% | 4.80% | 5.90% | 59.48% | NA |
| All Indica | 2759 | 1.80% | 1.20% | 3.33% | 93.73% | NA |
| All Japonica | 1512 | 80.60% | 12.20% | 4.50% | 2.65% | NA |
| Aus | 269 | 0.70% | 0.00% | 42.38% | 56.88% | NA |
| Indica I | 595 | 1.00% | 0.00% | 3.19% | 95.80% | NA |
| Indica II | 465 | 2.20% | 0.60% | 1.08% | 96.13% | NA |
| Indica III | 913 | 1.30% | 0.30% | 3.50% | 94.85% | NA |
| Indica Intermediate | 786 | 2.70% | 3.30% | 4.58% | 89.44% | NA |
| Temperate Japonica | 767 | 88.30% | 4.70% | 5.87% | 1.17% | NA |
| Tropical Japonica | 504 | 64.50% | 28.80% | 3.77% | 2.98% | NA |
| Japonica Intermediate | 241 | 90.00% | 1.70% | 1.66% | 6.64% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 55.60% | 11.10% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0136519596 | G -> A | LOC_Os01g63040.1 | missense_variant ; p.Pro380Leu; MODERATE | nonsynonymous_codon ; P380L | Average:4.947; most accessible tissue: Zhenshan97 root, score: 12.891 | possibly damaging  |
1.728 |
DELETERIOUS | 0.00 |
| vg0136519596 | G -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.947; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |