Search for Variation information by Variation ID:
Detailed information for vg0211848242:
| Variant ID: vg0211848242 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 11848242 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
GGGGGATTCTTTGCTAGTAATCAGCCAATTGGTAGGAGAATATGAATGCAAGAATGATACATTGATGGTTTATAATGAGAAGTGCCTAGAACTAATGAAA[G/C]
AGTTTCGGCTGGTTACTTTGAAGCATGTATCTCAGGAACAAAATCTTGAAGCTAATGATTTGGCTCAAGGGGCATCGGGGTATAAGCCGATGATCAAAGA
Reverse complement sequence
TCTTTGATCATCGGCTTATACCCCGATGCCCCTTGAGCCAAATCATTAGCTTCAAGATTTTGTTCCTGAGATACATGCTTCAAAGTAACCAGCCGAAACT[C/G]
TTTCATTAGTTCTAGGCACTTCTCATTATAAACCATCAATGTATCATTCTTGCATTCATATTCTCCTACCAATTGGCTGATTACTAGCAAAGAATCCCCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.80% | 7.90% | 9.23% | 0.00% | NA |
| All Indica | 2759 | 74.50% | 11.60% | 13.95% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Aus | 269 | 64.70% | 19.30% | 15.99% | 0.00% | NA |
| Indica I | 595 | 66.20% | 8.20% | 25.55% | 0.00% | NA |
| Indica II | 465 | 77.60% | 11.60% | 10.75% | 0.00% | NA |
| Indica III | 913 | 81.80% | 10.80% | 7.34% | 0.00% | NA |
| Indica Intermediate | 786 | 70.40% | 14.90% | 14.76% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 6.67% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0211848242 | G -> C | LOC_Os02g20110.1 | missense_variant ; p.Glu1615Gln; MODERATE | nonsynonymous_codon ; E1615Q | Average:18.137; most accessible tissue: Callus, score: 33.494 | benign  |
1.475 |
TOLERATED | 0.13 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0211848242 | NA | 1.57E-06 | mr1830 | 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 |
| vg0211848242 | NA | 2.33E-13 | mr1846 | 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 |
| vg0211848242 | 3.35E-06 | 3.98E-11 | mr1846 | 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 |
| vg0211848242 | NA | 1.74E-17 | mr1846_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 |
| vg0211848242 | NA | 6.33E-14 | mr1846_2 | 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 |