Search for Variation information by Variation ID:
Detailed information for vg0319757114:
| Variant ID: vg0319757114 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757114 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 295. )
Flanking Sequence (100 bp) in Reference Genome:
GCTAATGAGGCAAGAACCATGGTTGTTGGTGGTATCATCATCATTAGTATTGCTAGTGTTGTTGTCTGCATTGCGTCCATCTTCTTGGGGCAGGAACTCT[T/G]
GATGCACAACAGAAGATCCGGTGATCTGAAGTGGCTCAGTGCGCTGTCTTTGGTTACCACATGGAAATACTGGGATGTTGACAATCCTCCTCTTGCAGTT
Reverse complement sequence
AACTGCAAGAGGAGGATTGTCAACATCCCAGTATTTCCATGTGGTAACCAAAGACAGCGCACTGAGCCACTTCAGATCACCGGATCTTCTGTTGTGCATC[A/C]
AGAGTTCCTGCCCCAAGAAGATGGACGCAATGCAGACAACAACACTAGCAATACTAATGATGATGATACCACCAACAACCATGGTTCTTGCCTCATTAGC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.80% | 0.30% | 1.84% | 64.05% | NA |
| All Indica | 2759 | 6.40% | 0.60% | 1.74% | 91.30% | NA |
| All Japonica | 1512 | 83.40% | 0.00% | 1.98% | 14.62% | NA |
| Aus | 269 | 13.00% | 0.00% | 1.49% | 85.50% | NA |
| Indica I | 595 | 2.20% | 0.70% | 1.01% | 96.13% | NA |
| Indica II | 465 | 5.80% | 0.00% | 2.15% | 92.04% | NA |
| Indica III | 913 | 8.30% | 0.50% | 2.19% | 88.94% | NA |
| Indica Intermediate | 786 | 7.60% | 0.90% | 1.53% | 89.95% | NA |
| Temperate Japonica | 767 | 94.50% | 0.00% | 0.78% | 4.69% | NA |
| Tropical Japonica | 504 | 65.70% | 0.00% | 2.58% | 31.75% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 4.56% | 10.37% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 5.56% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757114 | T -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319757114 | T -> G | LOC_Os03g35670.1 | missense_variant ; p.Gln637Pro; MODERATE | nonsynonymous_codon ; Q637P | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.089 |
DELETERIOUS | 0.03 |