Search for Variation information by Variation ID:
Detailed information for vg1121624353:
| Variant ID: vg1121624353 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21624353 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATATCGAATACCCCAACGAATCGATCTGAAGTTGGAGTCGCTCCATGTTCCTTGTCGTTATCCCTGATGGGGACGTATGACTTAGGAGACAGAGCTTTCA[T/C]
GGCGCTGAGAAAGACCTTGCAGCTTGAGAGGTCGTGATTCTTTGTCTTCTGAATAGGACAATAGACATCACGAGTTGGAGAAATACGCTGAATTCCACGC
Reverse complement sequence
GCGTGGAATTCAGCGTATTTCTCCAACTCGTGATGTCTATTGTCCTATTCAGAAGACAAAGAATCACGACCTCTCAAGCTGCAAGGTCTTTCTCAGCGCC[A/G]
TGAAAGCTCTGTCTCCTAAGTCATACGTCCCCATCAGGGATAACGACAAGGAACATGGAGCGACTCCAACTTCAGATCGATTCGTTGGGGTATTCGATAT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.60% | 9.10% | 21.96% | 3.36% | NA |
| All Indica | 2759 | 61.80% | 7.10% | 29.07% | 1.99% | NA |
| All Japonica | 1512 | 78.60% | 13.80% | 2.84% | 4.70% | NA |
| Aus | 269 | 42.00% | 2.60% | 44.24% | 11.15% | NA |
| Indica I | 595 | 66.90% | 3.90% | 28.24% | 1.01% | NA |
| Indica II | 465 | 79.80% | 2.20% | 16.77% | 1.29% | NA |
| Indica III | 913 | 46.10% | 13.60% | 37.02% | 3.29% | NA |
| Indica Intermediate | 786 | 65.50% | 5.10% | 27.74% | 1.65% | NA |
| Temperate Japonica | 767 | 89.30% | 1.00% | 3.39% | 6.26% | NA |
| Tropical Japonica | 504 | 64.30% | 32.10% | 2.38% | 1.19% | NA |
| Japonica Intermediate | 241 | 74.70% | 16.20% | 2.07% | 7.05% | NA |
| VI/Aromatic | 96 | 36.50% | 8.30% | 54.17% | 1.04% | NA |
| Intermediate | 90 | 64.40% | 8.90% | 24.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1121624353 | T -> DEL | LOC_Os11g36640.1 | N | frameshift_variant | Average:14.726; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1121624353 | T -> C | LOC_Os11g36640.1 | missense_variant ; p.Met173Val; MODERATE | nonsynonymous_codon ; M173V | Average:14.726; most accessible tissue: Zhenshan97 root, score: 16.934 | benign  |
0.056 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121624353 | 2.42E-06 | 2.42E-06 | mr1756 | 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 |