Search for Variation information by Variation ID:
Detailed information for vg0334134011:
| Variant ID: vg0334134011 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34134011 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 354. )
Flanking Sequence (100 bp) in Reference Genome:
GAACATAAGGCCGACCACCGTACGAAGCCTAAACATCGCAGCGGGAAAACAGTGTTTGCTATGGTTAAAGATCTTAAAGTAGTGTTCGGAAAGGGGCCTG[G/A]
AAGCCAGCATATAGAGAGCGAAGATGGTCACGCGGCGATGTGGAAAAAGAACTCTATATTTTGGGAGTTACCATATTGGGAATTCTTGGACGTACGCCAC
Reverse complement sequence
GTGGCGTACGTCCAAGAATTCCCAATATGGTAACTCCCAAAATATAGAGTTCTTTTTCCACATCGCCGCGTGACCATCTTCGCTCTCTATATGCTGGCTT[C/T]
CAGGCCCCTTTCCGAACACTACTTTAAGATCTTTAACCATAGCAAACACTGTTTTCCCGCTGCGATGTTTAGGCTTCGTACGGTGGTCGGCCTTATGTTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.00% | 0.90% | 22.11% | 75.03% | NA |
| All Indica | 2759 | 1.80% | 0.90% | 25.30% | 72.06% | NA |
| All Japonica | 1512 | 0.80% | 0.10% | 15.08% | 84.06% | NA |
| Aus | 269 | 11.20% | 5.60% | 33.83% | 49.44% | NA |
| Indica I | 595 | 2.00% | 0.70% | 11.09% | 86.22% | NA |
| Indica II | 465 | 0.90% | 0.20% | 18.92% | 80.00% | NA |
| Indica III | 913 | 1.40% | 1.00% | 40.64% | 56.96% | NA |
| Indica Intermediate | 786 | 2.50% | 1.30% | 22.01% | 74.17% | NA |
| Temperate Japonica | 767 | 0.80% | 0.00% | 5.22% | 94.00% | NA |
| Tropical Japonica | 504 | 1.00% | 0.20% | 29.96% | 68.85% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 15.35% | 84.23% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 8.33% | 90.62% | NA |
| Intermediate | 90 | 3.30% | 0.00% | 22.22% | 74.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334134011 | G -> A | LOC_Os03g60010.1 | missense_variant ; p.Gly527Glu; MODERATE | nonsynonymous_codon ; G527E | Average:5.173; most accessible tissue: Minghui63 flower, score: 7.958 | probably damaging  |
2.272 |
DELETERIOUS | 0.01 |
| vg0334134011 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:5.173; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |