Search for Variation information by Variation ID:
Detailed information for vg0113688689:
| Variant ID: vg0113688689 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 13688689 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGTGAGCTTCGGCTTTTTGGTCTTTTGGGAACTAGATGACTCATCCTTGGCAATTTTATGATCTCCGGCCTTTGCATTATTGATCCTATTCTTGGGCCGA[G/A]
GATCCCCAATAATAACACTTTTCCCTTTCTTTTTGTCAACATTAATAGAACTAATAGGGAGAGGATCACTAACAATTCCGGTTTTAGGCATAGATGTAAC
Reverse complement sequence
GTTACATCTATGCCTAAAACCGGAATTGTTAGTGATCCTCTCCCTATTAGTTCTATTAATGTTGACAAAAAGAAAGGGAAAAGTGTTATTATTGGGGATC[C/T]
TCGGCCCAAGAATAGGATCAATAATGCAAAGGCCGGAGATCATAAAATTGCCAAGGATGAGTCATCTAGTTCCCAAAAGACCAAAAAGCCGAAGCTCACT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.20% | 4.80% | 2.96% | 7.98% | NA |
| All Indica | 2759 | 82.00% | 4.50% | 3.59% | 9.86% | NA |
| All Japonica | 1512 | 95.00% | 0.50% | 1.19% | 3.37% | NA |
| Aus | 269 | 50.20% | 29.40% | 2.97% | 17.47% | NA |
| Indica I | 595 | 67.70% | 1.30% | 4.71% | 26.22% | NA |
| Indica II | 465 | 89.70% | 6.20% | 3.23% | 0.86% | NA |
| Indica III | 913 | 88.70% | 4.50% | 1.97% | 4.82% | NA |
| Indica Intermediate | 786 | 80.50% | 6.00% | 4.83% | 8.65% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 86.90% | 1.40% | 3.37% | 8.33% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 71.90% | 11.50% | 14.58% | 2.08% | NA |
| Intermediate | 90 | 86.70% | 6.70% | 1.11% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0113688689 | G -> A | LOC_Os01g24294.1 | missense_variant ; p.Pro1241Leu; MODERATE | nonsynonymous_codon ; P1241L | Average:12.933; most accessible tissue: Minghui63 young leaf, score: 21.268 | benign  |
0.378 |
TOLERATED | 0.30 |
| vg0113688689 | G -> DEL | LOC_Os01g24294.1 | N | frameshift_variant | Average:12.933; most accessible tissue: Minghui63 young leaf, score: 21.268 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0113688689 | 4.43E-06 | 2.26E-06 | mr1210 | 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 |