Search for Variation information by Variation ID:
Detailed information for vg0407782160:
| Variant ID: vg0407782160 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 7782160 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTATTTCAGATGGTGATAACCAGGAGAACTGCTGCTACCGGTGATGGCAACCAACCCGAAGGTAGCAACACCAACATCCAAGGCGGCCCACCTCCACCT[C/G]
CTCCCCCGCCACCACCACCACCACCAGACACCAACCCCATCCTCACTCAAATCCTCGCCCAGCAGGCCAACATGATGGCTGCTTTCCTCCACCACATCCA
Reverse complement sequence
TGGATGTGGTGGAGGAAAGCAGCCATCATGTTGGCCTGCTGGGCGAGGATTTGAGTGAGGATGGGGTTGGTGTCTGGTGGTGGTGGTGGTGGCGGGGGAG[G/C]
AGGTGGAGGTGGGCCGCCTTGGATGTTGGTGTTGCTACCTTCGGGTTGGTTGCCATCACCGGTAGCAGCAGTTCTCCTGGTTATCACCATCTGAAATACC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.70% | 4.60% | 2.67% | 10.03% | NA |
| All Indica | 2759 | 87.30% | 3.40% | 3.44% | 5.84% | NA |
| All Japonica | 1512 | 72.90% | 7.70% | 1.12% | 18.32% | NA |
| Aus | 269 | 84.40% | 0.70% | 4.83% | 10.04% | NA |
| Indica I | 595 | 93.80% | 0.30% | 1.18% | 4.71% | NA |
| Indica II | 465 | 92.90% | 1.70% | 1.94% | 3.44% | NA |
| Indica III | 913 | 77.70% | 7.10% | 5.26% | 9.97% | NA |
| Indica Intermediate | 786 | 90.30% | 2.40% | 3.94% | 3.31% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.00% | 2.35% | NA |
| Tropical Japonica | 504 | 31.30% | 21.60% | 1.79% | 45.24% | NA |
| Japonica Intermediate | 241 | 80.90% | 2.90% | 3.32% | 12.86% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 85.60% | 4.40% | 1.11% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0407782160 | C -> DEL | LOC_Os04g13930.1 | N | frameshift_variant | Average:22.123; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |
| vg0407782160 | C -> G | LOC_Os04g13930.1 | missense_variant ; p.Pro250Ala; MODERATE | nonsynonymous_codon ; P250A | Average:22.123; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | benign  |
1.221 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0407782160 | 5.06E-06 | NA | mr1275 | 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 |
| vg0407782160 | 5.65E-07 | NA | mr1551 | 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 |