Search for Variation information by Variation ID:
Detailed information for vg0119650630:
| Variant ID: vg0119650630 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 19650630 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 209. )
Flanking Sequence (100 bp) in Reference Genome:
ACATGGCCTAATAAACCCCGCCTTCAACAACCGATCAATCTCCTCTTTGACTCGGTCATATAGTAAAGGATTAAAATGACGAGGTGGTTGTTTATAAGGC[T/C]
TAAAACCCGGTTTAATTGGAAGCCGATGCTCCACAAGCTCACGGCTAAGACCCGGCATCTCATGGTACTCCCATGCAAAGCAATCAACATACTCTTGAAT
Reverse complement sequence
ATTCAAGAGTATGTTGATTGCTTTGCATGGGAGTACCATGAGATGCCGGGTCTTAGCCGTGAGCTTGTGGAGCATCGGCTTCCAATTAAACCGGGTTTTA[A/G]
GCCTTATAAACAACCACCTCGTCATTTTAATCCTTTACTATATGACCGAGTCAAAGAGGAGATTGATCGGTTGTTGAAGGCGGGGTTTATTAGGCCATGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.80% | 24.80% | 4.06% | 4.32% | NA |
| All Indica | 2759 | 45.50% | 42.20% | 6.13% | 6.20% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.13% | 0.20% | NA |
| Aus | 269 | 83.30% | 0.00% | 5.95% | 10.78% | NA |
| Indica I | 595 | 42.20% | 42.40% | 7.23% | 8.24% | NA |
| Indica II | 465 | 74.40% | 7.50% | 8.17% | 9.89% | NA |
| Indica III | 913 | 28.40% | 67.60% | 2.74% | 1.31% | NA |
| Indica Intermediate | 786 | 50.80% | 33.10% | 8.02% | 8.14% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 8.90% | 5.56% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0119650630 | T -> DEL | LOC_Os01g35504.1 | N | frameshift_variant | Average:43.86; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0119650630 | T -> C | LOC_Os01g35504.1 | missense_variant ; p.Lys112Arg; MODERATE | nonsynonymous_codon ; K112R | Average:43.86; most accessible tissue: Zhenshan97 panicle, score: 68.538 | benign  |
-0.994 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0119650630 | NA | 9.90E-08 | mr1175_2 | 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 |
| vg0119650630 | NA | 9.00E-06 | mr1360_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 |
| vg0119650630 | NA | 4.25E-06 | mr1510_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 |
| vg0119650630 | NA | 4.69E-08 | mr1519_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 |
| vg0119650630 | NA | 2.93E-06 | mr1910_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 |