Search for Variation information by Variation ID:
Detailed information for vg0207793650:
| Variant ID: vg0207793650 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 7793650 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAACTGCTGGGACAAGTCCTCCCAGGAGTGAATGGAGTCGGGGGGCTGGGTCATTAACCAGCCACACGCCTGACCCTTGAGGGCCATGGGAAAGTAATTC[G/T]
CCATGACCCGGTCGTCACCCCCTGCAGCCACGATGACCGTGGTATAGATCTGGAGGAACTCGGAGGGATTGATGTTACCATCATACTTCTCCGTAAGGTT
Reverse complement sequence
AACCTTACGGAGAAGTATGATGGTAACATCAATCCCTCCGAGTTCCTCCAGATCTATACCACGGTCATCGTGGCTGCAGGGGGTGACGACCGGGTCATGG[C/A]
GAATTACTTTCCCATGGCCCTCAAGGGTCAGGCGTGTGGCTGGTTAATGACCCAGCCCCCCGACTCCATTCACTCCTGGGAGGACTTGTCCCAGCAGTTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.80% | 12.20% | 1.52% | 49.51% | NA |
| All Indica | 2759 | 6.90% | 8.50% | 2.43% | 82.20% | NA |
| All Japonica | 1512 | 97.20% | 0.30% | 0.07% | 2.38% | NA |
| Aus | 269 | 1.10% | 98.10% | 0.37% | 0.37% | NA |
| Indica I | 595 | 3.40% | 0.30% | 2.18% | 94.12% | NA |
| Indica II | 465 | 4.50% | 1.90% | 3.44% | 90.11% | NA |
| Indica III | 913 | 9.40% | 16.20% | 1.97% | 72.40% | NA |
| Indica Intermediate | 786 | 8.00% | 9.50% | 2.54% | 79.90% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 95.80% | 0.20% | 0.20% | 3.77% | NA |
| Japonica Intermediate | 241 | 96.70% | 1.70% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 39.60% | 60.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 17.80% | 3.33% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0207793650 | G -> T | LOC_Os02g14220.1 | missense_variant ; p.Ala284Glu; MODERATE | nonsynonymous_codon ; A284E | Average:9.707; most accessible tissue: Callus, score: 32.448 | possibly damaging  |
1.835 |
DELETERIOUS | 0.01 |
| vg0207793650 | G -> DEL | LOC_Os02g14220.1 | N | frameshift_variant | Average:9.707; most accessible tissue: Callus, score: 32.448 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0207793650 | NA | 4.86E-06 | mr1063 | 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 |
| vg0207793650 | 1.81E-06 | 7.77E-07 | mr1135 | 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 |
| vg0207793650 | NA | 1.08E-08 | mr1570 | 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 |
| vg0207793650 | NA | 1.94E-07 | mr1803 | 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 |
| vg0207793650 | NA | 3.44E-07 | mr1522_2 | 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 |