Search for Variation information by Variation ID:
Detailed information for vg0118949515:
| Variant ID: vg0118949515 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18949515 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.21, others allele: 0.00, population size: 34. )
Flanking Sequence (100 bp) in Reference Genome:
TAGATGCGTCTCACCGTCTCCTCCAGGGTAATCCAGCTCGAGGTCCTTGTACGCGCCTTCGACCAACTCAACTTCGACCTTGAAGTATCCTGCTGGAATC[A/G]
GCCTGTAGTGGTAAGTATCTGAAGGGTCCGTTGGGATGGCCATGCCCGACGCCACCTTCGTGTGGTGAGAGGTTATTTATTAGTAATCAACATATATAAG
Reverse complement sequence
CTTATATATGTTGATTACTAATAAATAACCTCTCACCACACGAAGGTGGCGTCGGGCATGGCCATCCCAACGGACCCTTCAGATACTTACCACTACAGGC[T/C]
GATTCCAGCAGGATACTTCAAGGTCGAAGTTGAGTTGGTCGAAGGCGCGTACAAGGACCTCGAGCTGGATTACCCTGGAGGAGACGGTGAGACGCATCTA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.60% | 0.20% | 14.24% | 43.91% | NA |
| All Indica | 2759 | 8.70% | 0.30% | 19.61% | 71.33% | NA |
| All Japonica | 1512 | 94.80% | 0.10% | 2.98% | 2.18% | NA |
| Aus | 269 | 52.00% | 0.00% | 30.48% | 17.47% | NA |
| Indica I | 595 | 1.80% | 0.30% | 31.60% | 66.22% | NA |
| Indica II | 465 | 6.50% | 0.00% | 12.26% | 81.29% | NA |
| Indica III | 913 | 11.70% | 0.50% | 14.79% | 72.95% | NA |
| Indica Intermediate | 786 | 11.80% | 0.30% | 20.48% | 67.43% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 86.30% | 0.20% | 8.93% | 4.56% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 65.60% | 1.10% | 5.56% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118949515 | A -> G | LOC_Os01g34374.1 | missense_variant ; p.Leu1398Pro; MODERATE | nonsynonymous_codon ; L1398P | Average:24.787; most accessible tissue: Callus, score: 40.073 | benign  |
-0.289 |
TOLERATED | 1.00 |
| vg0118949515 | A -> DEL | LOC_Os01g34374.1 | N | frameshift_variant | Average:24.787; most accessible tissue: Callus, score: 40.073 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0118949515 | 9.90E-07 | 8.21E-08 | 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 |
| vg0118949515 | NA | 6.86E-15 | mr1228 | 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 |
| vg0118949515 | NA | 1.49E-20 | mr1254 | 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 |
| vg0118949515 | NA | 1.26E-06 | mr1672 | 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 |
| vg0118949515 | NA | 3.44E-09 | mr1946_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 |
| vg0118949515 | NA | 3.44E-09 | mr1948_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 |