Search for Variation information by Variation ID:
Detailed information for vg0515291769:
| Variant ID: vg0515291769 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 15291769 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, C: 0.22, others allele: 0.00, population size: 85. )
Flanking Sequence (100 bp) in Reference Genome:
GAGCATAGGTTTGCAGACGTTAGGAATAGCTCTAAGAAGGTTAATCATGTTTGCCCGTACATGTATGGGTCGGATGATGATGAGGACGATTCTGAAATAG[T/C]
TGCAGCTGAATGGGTCAGGAGTAAAAAGGTCATACCATGCCAATGGGTAAAAAGTTCTGGAAAAGAGGAGAAGTATGACTTTGATATTACTAAAGCTGAC
Reverse complement sequence
GTCAGCTTTAGTAATATCAAAGTCATACTTCTCCTCTTTTCCAGAACTTTTTACCCATTGGCATGGTATGACCTTTTTACTCCTGACCCATTCAGCTGCA[A/G]
CTATTTCAGAATCGTCCTCATCATCATCCGACCCATACATGTACGGGCAAACATGATTAACCTTCTTAGAGCTATTCCTAACGTCTGCAAACCTATGCTC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.00% | 21.10% | 0.19% | 19.68% | NA |
| All Indica | 2759 | 79.50% | 6.70% | 0.22% | 13.63% | NA |
| All Japonica | 1512 | 23.50% | 46.90% | 0.20% | 29.43% | NA |
| Aus | 269 | 69.90% | 29.70% | 0.00% | 0.37% | NA |
| Indica I | 595 | 92.90% | 4.40% | 0.00% | 2.69% | NA |
| Indica II | 465 | 74.80% | 2.80% | 0.65% | 21.72% | NA |
| Indica III | 913 | 65.60% | 11.10% | 0.33% | 23.00% | NA |
| Indica Intermediate | 786 | 88.20% | 5.60% | 0.00% | 6.23% | NA |
| Temperate Japonica | 767 | 6.40% | 81.20% | 0.00% | 12.39% | NA |
| Tropical Japonica | 504 | 50.40% | 6.00% | 0.40% | 43.25% | NA |
| Japonica Intermediate | 241 | 21.60% | 23.20% | 0.41% | 54.77% | NA |
| VI/Aromatic | 96 | 5.20% | 4.20% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 52.20% | 24.40% | 0.00% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0515291769 | T -> DEL | LOC_Os05g26290.1 | N | frameshift_variant | Average:47.746; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| vg0515291769 | T -> C | LOC_Os05g26290.1 | missense_variant ; p.Val549Ala; MODERATE | nonsynonymous_codon ; V549A | Average:47.746; most accessible tissue: Minghui63 flag leaf, score: 77.153 | possibly damaging  |
-1.778 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0515291769 | NA | 1.54E-15 | mr1401 | 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 |
| vg0515291769 | NA | 1.11E-06 | mr1422 | 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 |
| vg0515291769 | NA | 3.24E-08 | mr1551 | 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 |
| vg0515291769 | NA | 5.50E-09 | mr1552 | 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 |
| vg0515291769 | NA | 1.25E-18 | mr1593 | 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 |
| vg0515291769 | NA | 9.07E-06 | mr1195_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 |
| vg0515291769 | NA | 4.02E-07 | mr1347_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 |
| vg0515291769 | NA | 2.14E-27 | mr1593_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 |
| vg0515291769 | NA | 7.68E-06 | mr1682_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 |