Search for Variation information by Variation ID:
Detailed information for vg0815410038:
| Variant ID: vg0815410038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15410038 |
| 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: 195. )
Flanking Sequence (100 bp) in Reference Genome:
CTGAGTGACTGTCCTTGGTGGGGTCCATTTGGTAACTGACTCCACATTTGCTGGATCCACAGCTACTCCTTGAGCATTCACGATGTGACCAAGAAACTGA[A/C]
CTTCCTTAAGCCAGAAGTCGCACTTGCTGAACTTGGCATATAGCTGGTGCTCTTTTAACTTTTCAAGTACCAGCCGAAGATGCTGCTCATGTTCTTCCTC
Reverse complement sequence
GAGGAAGAACATGAGCAGCATCTTCGGCTGGTACTTGAAAAGTTAAAAGAGCACCAGCTATATGCCAAGTTCAGCAAGTGCGACTTCTGGCTTAAGGAAG[T/G]
TCAGTTTCTTGGTCACATCGTGAATGCTCAAGGAGTAGCTGTGGATCCAGCAAATGTGGAGTCAGTTACCAAATGGACCCCACCAAGGACAGTCACTCAG
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 | 16.80% | 3.90% | 7.32% | 71.96% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 7.79% | 91.08% | NA |
| All Japonica | 1512 | 48.90% | 11.60% | 2.65% | 36.84% | NA |
| Aus | 269 | 2.20% | 0.00% | 29.00% | 68.77% | NA |
| Indica I | 595 | 0.70% | 0.00% | 0.34% | 98.99% | NA |
| Indica II | 465 | 1.90% | 0.00% | 5.81% | 92.26% | NA |
| Indica III | 913 | 0.30% | 0.00% | 13.36% | 86.31% | NA |
| Indica Intermediate | 786 | 1.80% | 0.10% | 8.14% | 89.95% | NA |
| Temperate Japonica | 767 | 60.80% | 21.30% | 2.61% | 15.38% | NA |
| Tropical Japonica | 504 | 32.50% | 0.40% | 1.79% | 65.28% | NA |
| Japonica Intermediate | 241 | 45.60% | 4.10% | 4.56% | 45.64% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 3.12% | 92.71% | NA |
| Intermediate | 90 | 16.70% | 8.90% | 11.11% | 63.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815410038 | A -> C | LOC_Os08g25330.1 | missense_variant ; p.Val783Gly; MODERATE | nonsynonymous_codon ; V783G | Average:4.486; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.154 |
DELETERIOUS | 0.00 |
| vg0815410038 | A -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:4.486; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |