Search for Variation information by Variation ID:
Detailed information for vg0719562787:
| Variant ID: vg0719562787 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562787 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 381. )
Flanking Sequence (100 bp) in Reference Genome:
GAGTTACCATATTGGGAATTCTTGGACGTACGCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAGGTGTAT[A/G]
CGGAAAGTCGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTAC
Reverse complement sequence
GTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCGACTTTCCG[T/C]
ATACACCTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGCGTACGTCCAAGAATTCCCAATATGGTAACTC
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 | 22.40% | 0.30% | 23.06% | 54.25% | NA |
| All Indica | 2759 | 1.70% | 0.00% | 17.33% | 80.97% | NA |
| All Japonica | 1512 | 65.50% | 0.90% | 27.31% | 6.35% | NA |
| Aus | 269 | 0.40% | 0.00% | 49.44% | 50.19% | NA |
| Indica I | 595 | 0.30% | 0.00% | 4.71% | 94.96% | NA |
| Indica II | 465 | 3.70% | 0.00% | 8.82% | 87.53% | NA |
| Indica III | 913 | 0.90% | 0.00% | 30.67% | 68.46% | NA |
| Indica Intermediate | 786 | 2.50% | 0.00% | 16.41% | 81.04% | NA |
| Temperate Japonica | 767 | 93.10% | 0.40% | 4.56% | 1.96% | NA |
| Tropical Japonica | 504 | 29.40% | 1.20% | 58.13% | 11.31% | NA |
| Japonica Intermediate | 241 | 53.10% | 1.70% | 35.27% | 9.96% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 44.79% | 50.00% | NA |
| Intermediate | 90 | 16.70% | 1.10% | 25.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562787 | A -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0719562787 | A -> G | LOC_Os07g32740.1 | missense_variant ; p.Tyr535Cys; MODERATE | nonsynonymous_codon ; Y535C | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | probably damaging  |
3.347 |
DELETERIOUS | 0.01 |