Search for Variation information by Variation ID:
Detailed information for vg0139407380:
| Variant ID: vg0139407380 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39407380 |
| 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: 111. )
Flanking Sequence (100 bp) in Reference Genome:
TCCTGAACATGGGCCTCAAGGCCGAACTTGCCGAGGACCGATTCGAAGCTGCAGCGCCACTGGCTGTAGTTGGAGACGTCGAGATCGAGGACGACCGGGA[C/T]
GTGGGAGCGGATGTTGACGGTTTGAAGAACAGAGGTGGAAGGCGCCGGCACAGGCTCTTCGTCAGAGGTGGACGAGGCGTCGGAAGCGCCGGAGCTGTGC
Reverse complement sequence
GCACAGCTCCGGCGCTTCCGACGCCTCGTCCACCTCTGACGAAGAGCCTGTGCCGGCGCCTTCCACCTCTGTTCTTCAAACCGTCAACATCCGCTCCCAC[G/A]
TCCCGGTCGTCCTCGATCTCGACGTCTCCAACTACAGCCAGTGGCGCTGCAGCTTCGAATCGGTCCTCGGCAAGTTCGGCCTTGAGGCCCATGTTCAGGA
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 | 20.20% | 0.10% | 7.58% | 72.03% | NA |
| All Indica | 2759 | 0.80% | 0.00% | 1.12% | 98.12% | NA |
| All Japonica | 1512 | 59.70% | 0.50% | 21.03% | 18.78% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.37% | 99.63% | NA |
| Indica I | 595 | 1.00% | 0.00% | 1.18% | 97.82% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.22% | 99.14% | NA |
| Indica III | 913 | 0.00% | 0.00% | 0.11% | 99.89% | NA |
| Indica Intermediate | 786 | 1.50% | 0.00% | 2.80% | 95.67% | NA |
| Temperate Japonica | 767 | 54.60% | 0.00% | 34.29% | 11.08% | NA |
| Tropical Japonica | 504 | 66.10% | 0.20% | 2.78% | 30.95% | NA |
| Japonica Intermediate | 241 | 62.70% | 2.50% | 17.01% | 17.84% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 0.00% | 97.92% | NA |
| Intermediate | 90 | 34.40% | 0.00% | 8.89% | 56.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139407380 | C -> T | LOC_Os01g67800.1 | missense_variant ; p.Val36Ile; MODERATE | nonsynonymous_codon ; V36I | Average:12.604; most accessible tissue: Zhenshan97 flower, score: 31.8 | benign  |
0.494 |
TOLERATED | 0.41 |
| vg0139407380 | C -> DEL | LOC_Os01g67800.1 | N | frameshift_variant | Average:12.604; most accessible tissue: Zhenshan97 flower, score: 31.8 | N | N | N | N |