Search for Variation information by Variation ID:
Detailed information for vg0727003262:
| Variant ID: vg0727003262 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27003262 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 359. )
Flanking Sequence (100 bp) in Reference Genome:
GCTTGATGCTATAGAGGACCTCCAGAATAACCCTCAAGAACAAGAACCACACACATGGAGAGACATACAAAGCAGGTGGTGCATCGAACACCTTACTGAA[A/C]
ACTTATCTGCACATTTTGGTGGCAAGAAGTCGGCGGTGCTGTTCAATAAACTCTGTCAGCAGAGCCAACCAAGTAAGTTTACTGATATCTGGAAGGACCT
Reverse complement sequence
AGGTCCTTCCAGATATCAGTAAACTTACTTGGTTGGCTCTGCTGACAGAGTTTATTGAACAGCACCGCCGACTTCTTGCCACCAAAATGTGCAGATAAGT[T/G]
TTCAGTAAGGTGTTCGATGCACCACCTGCTTTGTATGTCTCTCCATGTGTGTGGTTCTTGTTCTTGAGGGTTATTCTGGAGGTCCTCTATAGCATCAAGC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.20% | 0.30% | 11.28% | 1.25% | NA |
| All Indica | 2759 | 97.30% | 0.00% | 2.65% | 0.07% | NA |
| All Japonica | 1512 | 66.20% | 0.80% | 29.23% | 3.77% | NA |
| Aus | 269 | 98.90% | 0.00% | 1.12% | 0.00% | NA |
| Indica I | 595 | 95.50% | 0.00% | 4.54% | 0.00% | NA |
| Indica II | 465 | 98.90% | 0.00% | 1.08% | 0.00% | NA |
| Indica III | 913 | 98.70% | 0.00% | 1.31% | 0.00% | NA |
| Indica Intermediate | 786 | 96.10% | 0.00% | 3.69% | 0.25% | NA |
| Temperate Japonica | 767 | 70.40% | 0.40% | 22.03% | 7.17% | NA |
| Tropical Japonica | 504 | 48.80% | 1.80% | 49.01% | 0.40% | NA |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 10.79% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 16.67% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0727003262 | A -> DEL | LOC_Os07g45250.1 | N | frameshift_variant | Average:60.987; most accessible tissue: Callus, score: 87.142 | N | N | N | N |
| vg0727003262 | A -> C | LOC_Os07g45250.1 | missense_variant ; p.Asn400His; MODERATE | nonsynonymous_codon | Average:60.987; most accessible tissue: Callus, score: 87.142 | probably damaging  |
2.356 |
DELETERIOUS | 0.01 |