Search for Variation information by Variation ID:
Detailed information for vg0114126056:
| Variant ID: vg0114126056 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14126056 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGGCACTTTACTGGACATCCCGAGTAAGACGAAAGATGGGTTGAAGTCCCGGACCGACCTCGTCAATTTGGACATAAGGCGTGGGCTTCACCCCAAAGAG[C/A]
TGCCAAATGGGAAGATCGAAATTCCTCCGGCTTGCTACTCACTAACACCTGACGAGAAAAAATCTTTATGTAGATGCTTGCATAGTGTGAAAGTCCCGAC
Reverse complement sequence
GTCGGGACTTTCACACTATGCAAGCATCTACATAAAGATTTTTTCTCGTCAGGTGTTAGTGAGTAGCAAGCCGGAGGAATTTCGATCTTCCCATTTGGCA[G/T]
CTCTTTGGGGTGAAGCCCACGCCTTATGTCCAAATTGACGAGGTCGGTCCGGGACTTCAACCCATCTTTCGTCTTACTCGGGATGTCCAGTAAAGTGCCA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.20% | 1.30% | 17.05% | 2.41% | NA |
| All Indica | 2759 | 69.00% | 1.90% | 26.06% | 2.97% | NA |
| All Japonica | 1512 | 95.90% | 0.30% | 2.58% | 1.19% | NA |
| Aus | 269 | 92.20% | 0.00% | 7.81% | 0.00% | NA |
| Indica I | 595 | 77.80% | 0.50% | 17.98% | 3.70% | NA |
| Indica II | 465 | 72.70% | 0.00% | 21.08% | 6.24% | NA |
| Indica III | 913 | 60.10% | 3.80% | 35.27% | 0.77% | NA |
| Indica Intermediate | 786 | 70.60% | 1.90% | 24.43% | 3.05% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.26% | 1.43% | NA |
| Tropical Japonica | 504 | 90.90% | 1.00% | 6.94% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 71.90% | 1.00% | 14.58% | 12.50% | NA |
| Intermediate | 90 | 81.10% | 2.20% | 14.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0114126056 | C -> A | LOC_Os01g25040.1 | missense_variant ; p.Leu785Met; MODERATE | nonsynonymous_codon ; L785M | Average:13.629; most accessible tissue: Callus, score: 29.275 | probably damaging  |
2.332 |
TOLERATED | 0.09 |
| vg0114126056 | C -> DEL | LOC_Os01g25040.1 | N | frameshift_variant | Average:13.629; most accessible tissue: Callus, score: 29.275 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114126056 | NA | 4.49E-07 | mr1030 | 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 |
| vg0114126056 | NA | 2.65E-06 | mr1098 | 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 |
| vg0114126056 | NA | 1.71E-06 | mr1192 | Ind_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 |
| vg0114126056 | NA | 3.60E-06 | mr1621 | 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 |