Search for Variation information by Variation ID:
Detailed information for vg1109649685:
| Variant ID: vg1109649685 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9649685 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAATTGAAAACACATGAGATGAATATTCTTTCTCGCAAAGTTGATTCTAAATCGAGTGCCTTGGTTTCTTCTTCTTCTTCTTTGGATGTTGATGCTTCTT[C/T]
ATCTAAGTCGTTTTTTCTTGCTGTTTTTAATGCCACATCCGATGATCAACTCGAACAAATCGAGGAGGACGATTTAGCTTTGGTTGCTAACAGAATTGCT
Reverse complement sequence
AGCAATTCTGTTAGCAACCAAAGCTAAATCGTCCTCCTCGATTTGTTCGAGTTGATCATCGGATGTGGCATTAAAAACAGCAAGAAAAAACGACTTAGAT[G/A]
AAGAAGCATCAACATCCAAAGAAGAAGAAGAAGAAACCAAGGCACTCGATTTAGAATCAACTTTGCGAGAAAGAATATTCATCTCATGTGTTTTCAATTT
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 | 68.90% | 0.10% | 1.12% | 29.86% | NA |
| All Indica | 2759 | 55.20% | 0.10% | 1.63% | 43.06% | NA |
| All Japonica | 1512 | 97.20% | 0.10% | 0.13% | 2.58% | NA |
| Aus | 269 | 39.00% | 0.00% | 1.86% | 59.11% | NA |
| Indica I | 595 | 46.70% | 0.00% | 2.02% | 51.26% | NA |
| Indica II | 465 | 57.40% | 0.00% | 1.51% | 41.08% | NA |
| Indica III | 913 | 60.50% | 0.30% | 1.31% | 37.90% | NA |
| Indica Intermediate | 786 | 54.10% | 0.10% | 1.78% | 44.02% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.26% | 2.35% | NA |
| Tropical Japonica | 504 | 96.60% | 0.00% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 1.11% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109649685 | C -> T | LOC_Os11g17310.1 | missense_variant ; p.Ser228Leu; MODERATE | nonsynonymous_codon ; S228L | Average:5.549; most accessible tissue: Callus, score: 13.393 | possibly damaging  |
1.521 |
DELETERIOUS | 0.03 |
| vg1109649685 | C -> DEL | LOC_Os11g17310.1 | N | frameshift_variant | Average:5.549; most accessible tissue: Callus, score: 13.393 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1109649685 | 1.75E-06 | 1.75E-06 | mr1384 | Ind_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 |