Search for Variation information by Variation ID:
Detailed information for vg1007739811:
| Variant ID: vg1007739811 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7739811 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
TTGGTGTACATCTTGTGTATTAGGTTCTGCCATGCCTGCGGCTTGGGGGAGTTGGAGGTGATGGTGAACGCTGCCATCTCCTCCAAGCAGCTCTCAAGAA[A/G]
CACACGAACCTCCATATCGGTCCACCGGCTACGGCCATCGCCCATCTACTCCGTGCAAGTCAAATAAAATTGAATCGGAAATGAACAAATTAATACAAAC
Reverse complement sequence
GTTTGTATTAATTTGTTCATTTCCGATTCAATTTTATTTGACTTGCACGGAGTAGATGGGCGATGGCCGTAGCCGGTGGACCGATATGGAGGTTCGTGTG[T/C]
TTCTTGAGAGCTGCTTGGAGGAGATGGCAGCGTTCACCATCACCTCCAACTCCCCCAAGCCGCAGGCATGGCAGAACCTAATACACAAGATGTACACCAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.40% | 0.10% | 0.28% | 6.24% | NA |
| All Indica | 2759 | 99.20% | 0.10% | 0.14% | 0.58% | NA |
| All Japonica | 1512 | 81.20% | 0.00% | 0.60% | 18.19% | 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 | 98.30% | 0.00% | 0.43% | 1.29% | NA |
| Indica III | 913 | 99.10% | 0.30% | 0.00% | 0.55% | NA |
| Indica Intermediate | 786 | 99.10% | 0.00% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 81.00% | 0.00% | 0.91% | 18.12% | NA |
| Tropical Japonica | 504 | 84.50% | 0.00% | 0.20% | 15.28% | NA |
| Japonica Intermediate | 241 | 75.10% | 0.00% | 0.41% | 24.48% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007739811 | A -> G | LOC_Os10g14290.1 | missense_variant ; p.Phe125Leu; MODERATE | nonsynonymous_codon ; F125L | Average:5.203; most accessible tissue: Callus, score: 12.568 | benign  |
1.293 |
DELETERIOUS | 0.00 |
| vg1007739811 | A -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:5.203; most accessible tissue: Callus, score: 12.568 | N | N | N | N |