Search for Variation information by Variation ID:
Detailed information for vg1114869858:
| Variant ID: vg1114869858 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14869858 |
| Reference Allele: T | Alternative Allele: G,C |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )
Flanking Sequence (100 bp) in Reference Genome:
AGTCGTTGCTCCACAGAAAACTCTACCGACAAAGAAACCAGCCGTACCAACGCCACTGACCTTCAAGACAATGGCCAGCAAGACTCTTCGCGAGTTCGCT[T/G,C]
TTCCCTCTGCTGACAATGTGGCCGTCGAGCCACAAGTCAACATAGGAGATGTGGATTTCGATTTGAAGTCCAGCCTCATCATGATGGCGCAGGCTAGCCT
Reverse complement sequence
AGGCTAGCCTGCGCCATCATGATGAGGCTGGACTTCAAATCGAAATCCACATCTCCTATGTTGACTTGTGGCTCGACGGCCACATTGTCAGCAGAGGGAA[A/C,G]
AGCGAACTCGCGAAGAGTCTTGCTGGCCATTGTCTTGAAGGTCAGTGGCGTTGGTACGGCTGGTTTCTTTGTCGGTAGAGTTTTCTGTGGAGCAACGACT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.00% | 8.50% | 37.71% | 25.56% | C: 0.23% |
| All Indica | 2759 | 2.90% | 1.80% | 55.56% | 39.36% | C: 0.40% |
| All Japonica | 1512 | 74.50% | 22.40% | 1.72% | 1.32% | NA |
| Aus | 269 | 0.70% | 0.40% | 69.14% | 29.74% | NA |
| Indica I | 595 | 4.00% | 1.80% | 37.48% | 56.47% | C: 0.17% |
| Indica II | 465 | 2.40% | 0.20% | 52.04% | 45.38% | NA |
| Indica III | 913 | 1.90% | 0.90% | 72.51% | 23.99% | C: 0.77% |
| Indica Intermediate | 786 | 3.40% | 3.80% | 51.65% | 40.71% | C: 0.38% |
| Temperate Japonica | 767 | 60.50% | 36.10% | 1.43% | 1.96% | NA |
| Tropical Japonica | 504 | 95.80% | 0.80% | 2.58% | 0.79% | NA |
| Japonica Intermediate | 241 | 74.70% | 24.10% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 84.40% | 6.20% | 6.25% | 3.12% | NA |
| Intermediate | 90 | 40.00% | 4.40% | 34.44% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114869858 | T -> DEL | LOC_Os11g26000.1 | N | frameshift_variant | Average:13.618; most accessible tissue: Callus, score: 19.394 | N | N | N | N |
| vg1114869858 | T -> G | LOC_Os11g26000.1 | missense_variant ; p.Phe11Val; MODERATE | nonsynonymous_codon ; F11A | Average:13.618; most accessible tissue: Callus, score: 19.394 | probably damaging  |
-2.378 |
TOLERATED | 1.00 |
| vg1114869858 | T -> C | LOC_Os11g26000.1 | missense_variant ; p.Phe11Leu; MODERATE | nonsynonymous_codon ; F11L | Average:13.618; most accessible tissue: Callus, score: 19.394 | benign |
-0.934 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1114869858 | NA | 3.69E-07 | mr1028 | 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 |
| vg1114869858 | 2.08E-06 | 1.14E-06 | mr1230 | 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 |
| vg1114869858 | NA | 4.58E-08 | mr1382 | 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 |
| vg1114869858 | NA | 4.00E-06 | mr1382 | 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 |
| vg1114869858 | 7.76E-06 | 1.24E-07 | mr1424 | 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 |
| vg1114869858 | 9.77E-06 | 9.76E-06 | mr1424 | 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 |
| vg1114869858 | NA | 5.99E-07 | mr1453 | 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 |