Search for Variation information by Variation ID:
Detailed information for vg0719562676:
| Variant ID: vg0719562676 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562676 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 354. )
Flanking Sequence (100 bp) in Reference Genome:
TTTGCTATGGTTAAAGATCTTAAAGTAGTGTTCGGAAAGGGGCCTGGAAGCCAGCATATAGAGAGCGAAGATGGTCACGCGGCGATGTGGAAAAAGAACT[C/A]
TATATTTTGGGAGTTACCATATTGGGAATTCTTGGACGTACGCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTC
Reverse complement sequence
GAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGCGTACGTCCAAGAATTCCCAATATGGTAACTCCCAAAATATA[G/T]
AGTTCTTTTTCCACATCGCCGCGTGACCATCTTCGCTCTCTATATGCTGGCTTCCAGGCCCCTTTCCGAACACTACTTTAAGATCTTTAACCATAGCAAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.80% | 0.10% | 23.61% | 56.50% | NA |
| All Indica | 2759 | 1.20% | 0.00% | 21.38% | 77.42% | NA |
| All Japonica | 1512 | 58.80% | 0.30% | 21.83% | 19.05% | NA |
| Aus | 269 | 0.00% | 0.00% | 64.68% | 35.32% | NA |
| Indica I | 595 | 1.00% | 0.00% | 2.86% | 96.13% | NA |
| Indica II | 465 | 1.70% | 0.00% | 18.71% | 79.57% | NA |
| Indica III | 913 | 0.40% | 0.00% | 38.34% | 61.23% | NA |
| Indica Intermediate | 786 | 1.90% | 0.00% | 17.30% | 80.79% | NA |
| Temperate Japonica | 767 | 92.60% | 0.70% | 2.35% | 4.43% | NA |
| Tropical Japonica | 504 | 10.50% | 0.00% | 54.96% | 34.52% | NA |
| Japonica Intermediate | 241 | 52.30% | 0.00% | 14.52% | 33.20% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 21.11% | 64.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562676 | C -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.947; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0719562676 | C -> A | LOC_Os07g32740.1 | missense_variant ; p.Ser498Tyr; MODERATE | nonsynonymous_codon ; S498Y | Average:4.947; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
0.587 |
DELETERIOUS | 0.01 |