Search for Variation information by Variation ID:
Detailed information for vg1108620178:
| Variant ID: vg1108620178 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8620178 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
TTTCAGTCTCCAATACCGCAGAAGCTAGGGATCAGTCTGAACCAGGCTACTGGTGAAGAACAAGAGGTAGCAGTGGAGAAAACCACTAAGAAGTTGGAGG[A/T]
TATTCCCATAGTCAGAGAGTATCCAGAGGTTTTTCCGGACGATCTGACAACAATGCCACCAAAAAGGGATATCGAGTTCCGGATTGACTTGGTACCTGGA
Reverse complement sequence
TCCAGGTACCAAGTCAATCCGGAACTCGATATCCCTTTTTGGTGGCATTGTTGTCAGATCGTCCGGAAAAACCTCTGGATACTCTCTGACTATGGGAATA[T/A]
CCTCCAACTTCTTAGTGGTTTTCTCCACTGCTACCTCTTGTTCTTCACCAGTAGCCTGGTTCAGACTGATCCCTAGCTTCTGCGGTATTGGAGACTGAAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.90% | 7.30% | 5.88% | 3.91% | NA |
| All Indica | 2759 | 75.50% | 8.70% | 9.31% | 6.49% | NA |
| All Japonica | 1512 | 92.70% | 6.20% | 0.86% | 0.26% | NA |
| Aus | 269 | 96.70% | 1.90% | 1.49% | 0.00% | NA |
| Indica I | 595 | 79.30% | 13.60% | 4.71% | 2.35% | NA |
| Indica II | 465 | 70.30% | 0.90% | 17.20% | 11.61% | NA |
| Indica III | 913 | 74.40% | 11.50% | 7.67% | 6.46% | NA |
| Indica Intermediate | 786 | 77.00% | 6.40% | 10.05% | 6.62% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 82.70% | 15.90% | 1.19% | 0.20% | NA |
| Japonica Intermediate | 241 | 91.30% | 4.60% | 2.90% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 8.90% | 4.44% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108620178 | A -> T | LOC_Os11g15260.1 | missense_variant ; p.Asp514Val; MODERATE | nonsynonymous_codon ; D514V | Average:22.532; most accessible tissue: Zhenshan97 panicle, score: 36.038 | probably damaging  |
2.003 |
DELETERIOUS | 0.00 |
| vg1108620178 | A -> DEL | LOC_Os11g15260.1 | N | frameshift_variant | Average:22.532; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108620178 | NA | 5.23E-07 | mr1136 | Jap_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 |
| vg1108620178 | 3.50E-07 | NA | mr1055_2 | Jap_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 |
| vg1108620178 | 9.12E-06 | NA | mr1132_2 | Jap_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 |