Search for Variation information by Variation ID:
Detailed information for vg0814299698:
| Variant ID: vg0814299698 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14299698 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 94. )
Flanking Sequence (100 bp) in Reference Genome:
ACAACAATGGAGAAAATCCCACACTTGCCCAAGTCCTGGCTCAACAGGCACAGCTTATGAACATGATGATACAGCAACTCCAGAACCAGCAGAACCAGGG[A/G,C]
AATAACCATGCGCCTCCCCAGAACAAGTTAGCAGAATTTCTTCGTGTAAGGCCGCCCACTTTCTCTAGTACCACTAATCCTGTTGAAGCTGGTGATTGGC
Reverse complement sequence
GCCAATCACCAGCTTCAACAGGATTAGTGGTACTAGAGAAAGTGGGCGGCCTTACACGAAGAAATTCTGCTAACTTGTTCTGGGGAGGCGCATGGTTATT[T/C,G]
CCCTGGTTCTGCTGGTTCTGGAGTTGCTGTATCATCATGTTCATAAGCTGTGCCTGTTGAGCCAGGACTTGGGCAAGTGTGGGATTTTCTCCATTGTTGT
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 | 43.80% | 9.20% | 16.63% | 30.11% | C: 0.23% |
| All Indica | 2759 | 29.20% | 15.50% | 13.12% | 42.19% | C: 0.04% |
| All Japonica | 1512 | 62.20% | 0.50% | 21.89% | 14.95% | C: 0.53% |
| Aus | 269 | 94.40% | 0.00% | 1.12% | 4.46% | NA |
| Indica I | 595 | 13.80% | 14.80% | 11.76% | 59.66% | NA |
| Indica II | 465 | 17.40% | 22.80% | 16.77% | 42.80% | C: 0.22% |
| Indica III | 913 | 48.30% | 9.70% | 10.51% | 31.43% | NA |
| Indica Intermediate | 786 | 25.60% | 18.30% | 15.01% | 41.09% | NA |
| Temperate Japonica | 767 | 86.20% | 0.70% | 10.56% | 2.61% | NA |
| Tropical Japonica | 504 | 35.90% | 0.20% | 27.78% | 34.92% | C: 1.19% |
| Japonica Intermediate | 241 | 40.70% | 0.40% | 45.64% | 12.45% | C: 0.83% |
| VI/Aromatic | 96 | 27.10% | 0.00% | 71.88% | 0.00% | C: 1.04% |
| Intermediate | 90 | 48.90% | 3.30% | 23.33% | 23.33% | C: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814299698 | A -> G | LOC_Os08g23620.1 | synonymous_variant ; p.Gly441Gly; LOW | synonymous_codon | Average:13.733; most accessible tissue: Callus, score: 29.743 | N | N | N | N |
| vg0814299698 | A -> C | LOC_Os08g23620.1 | synonymous_variant ; p.Gly441Gly; LOW | nonsynonymous_codon ; G441L | Average:13.733; most accessible tissue: Callus, score: 29.743 | probably damaging  |
2.25 |
DELETERIOUS | 0.00 |
| vg0814299698 | A -> DEL | LOC_Os08g23620.1 | N | frameshift_variant | Average:13.733; most accessible tissue: Callus, score: 29.743 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0814299698 | NA | 3.35E-06 | mr1193_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0814299698 | 4.79E-06 | NA | mr1338_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |