Search for Variation information by Variation ID:
Detailed information for vg0515429615:
| Variant ID: vg0515429615 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 15429615 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCAATGATGAGGAGAAAGTCATCTTCGCCGCTCACCAACTGCAGGGGCCCGCATCTCTATGGTGGGACCACTTCCAGGCTACGCAGCCAGAGGGACAGC[C/T]
TATCACCTGGGCCCGTTTCACTGCCGCCTTCCGGAGGACCCATGTGCCCGCCGGAGTCATGGCCCTTAAGAAGAGGGAATTTCGGGAGTTGAAACAAGGC
Reverse complement sequence
GCCTTGTTTCAACTCCCGAAATTCCCTCTTCTTAAGGGCCATGACTCCGGCGGGCACATGGGTCCTCCGGAAGGCGGCAGTGAAACGGGCCCAGGTGATA[G/A]
GCTGTCCCTCTGGCTGCGTAGCCTGGAAGTGGTCCCACCATAGAGATGCGGGCCCCTGCAGTTGGTGAGCGGCGAAGATGACTTTCTCCTCATCATTGCA
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 | 48.80% | 2.80% | 33.92% | 14.41% | NA |
| All Indica | 2759 | 46.50% | 4.10% | 45.56% | 3.91% | NA |
| All Japonica | 1512 | 49.50% | 1.30% | 13.96% | 35.25% | NA |
| Aus | 269 | 81.80% | 0.40% | 17.47% | 0.37% | NA |
| Indica I | 595 | 32.90% | 7.20% | 53.11% | 6.72% | NA |
| Indica II | 465 | 58.10% | 1.90% | 34.41% | 5.59% | NA |
| Indica III | 913 | 48.50% | 3.90% | 46.77% | 0.77% | NA |
| Indica Intermediate | 786 | 47.50% | 3.10% | 45.04% | 4.45% | NA |
| Temperate Japonica | 767 | 82.50% | 0.00% | 3.78% | 13.69% | NA |
| Tropical Japonica | 504 | 9.50% | 3.20% | 27.18% | 60.12% | NA |
| Japonica Intermediate | 241 | 27.80% | 1.70% | 18.67% | 51.87% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 58.33% | 30.21% | NA |
| Intermediate | 90 | 52.20% | 1.10% | 35.56% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0515429615 | C -> T | LOC_Os05g26560.1 | missense_variant ; p.Pro97Leu; MODERATE | nonsynonymous_codon ; P97L | Average:30.13; most accessible tissue: Minghui63 young leaf, score: 51.901 | possibly damaging  |
1.786 |
DELETERIOUS | 0.00 |
| vg0515429615 | C -> DEL | LOC_Os05g26560.1 | N | frameshift_variant | Average:30.13; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0515429615 | NA | 3.93E-07 | mr1739 | 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 |
| vg0515429615 | NA | 6.72E-08 | mr1951 | 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 |
| vg0515429615 | 2.81E-06 | 5.20E-11 | mr1676_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 |
| vg0515429615 | NA | 2.07E-09 | mr1916_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 |