Search for Variation information by Variation ID:
Detailed information for vg0235469783:
| Variant ID: vg0235469783 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 35469783 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, C: 0.26, others allele: 0.00, population size: 86. )
Flanking Sequence (100 bp) in Reference Genome:
TGGGGTGCTCCGGTCATTTTTGTGGAGAAAAAGGATAAGACGAAAAGGATGTGCGTTGATTATCGCGCACTCAACGAGGTCACAATCAAGAATAAATATC[A/C]
TTTACCGCGGATCGATGATTTGTTTGATCAACTGAAGGGAGCTAAGGTGTTCTCTAAGATAGACCTGCGATCAGGCTACCACTAGTTAAGGATCCGGGAA
Reverse complement sequence
TTCCCGGATCCTTAACTAGTGGTAGCCTGATCGCAGGTCTATCTTAGAGAACACCTTAGCTCCCTTCAGTTGATCAAACAAATCATCGATCCGCGGTAAA[T/G]
GATATTTATTCTTGATTGTGACCTCGTTGAGTGCGCGATAATCAACGCACATCCTTTTCGTCTTATCCTTTTTCTCCACAAAAATGACCGGAGCACCCCA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.40% | 4.70% | 40.80% | 17.16% | NA |
| All Indica | 2759 | 5.30% | 4.60% | 63.97% | 26.06% | NA |
| All Japonica | 1512 | 93.50% | 0.20% | 1.26% | 5.09% | NA |
| Aus | 269 | 32.00% | 27.90% | 38.66% | 1.49% | NA |
| Indica I | 595 | 5.50% | 10.40% | 66.05% | 17.98% | NA |
| Indica II | 465 | 5.40% | 2.80% | 49.68% | 42.15% | NA |
| Indica III | 913 | 3.80% | 1.60% | 73.82% | 20.70% | NA |
| Indica Intermediate | 786 | 6.90% | 4.80% | 59.41% | 28.88% | NA |
| Temperate Japonica | 767 | 92.60% | 0.10% | 0.65% | 6.65% | NA |
| Tropical Japonica | 504 | 94.80% | 0.20% | 1.98% | 2.98% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.40% | 1.66% | 4.56% | NA |
| VI/Aromatic | 96 | 76.00% | 9.40% | 13.54% | 1.04% | NA |
| Intermediate | 90 | 52.20% | 6.70% | 30.00% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0235469783 | A -> DEL | LOC_Os02g57930.1 | N | frameshift_variant | Average:11.894; most accessible tissue: Callus, score: 38.761 | N | N | N | N |
| vg0235469783 | A -> C | LOC_Os02g57930.1 | missense_variant ; p.His877Pro; MODERATE | nonsynonymous_codon ; H877P | Average:11.894; most accessible tissue: Callus, score: 38.761 | probably damaging  |
-3.205 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0235469783 | 6.64E-06 | NA | mr1218 | 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 |
| vg0235469783 | 4.70E-07 | NA | mr1218 | 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 |
| vg0235469783 | NA | 9.62E-18 | mr1566 | 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 |
| vg0235469783 | NA | 1.70E-12 | mr1553_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 |