Search for Variation information by Variation ID:
Detailed information for vg0610766790:
| Variant ID: vg0610766790 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10766790 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 295. )
Flanking Sequence (100 bp) in Reference Genome:
CGATTTGGTCTAATCACTTGTTTCTTTTACAGCCTCCTCCTCCTCCTTCACCCCTATGCAGCCAGAATCAAGCCATCGCCCTCCATCGGCTGCTGGTAGT[T/C]
ATAATGTTGAAGAAGAAGAACAACCAGCTGCTCCTGCTATCCAAGTAAGTTTTTGCCACTATAATTCCTAGATCGGCTGAATAACATTCAACACTAACTA
Reverse complement sequence
TAGTTAGTGTTGAATGTTATTCAGCCGATCTAGGAATTATAGTGGCAAAAACTTACTTGGATAGCAGGAGCAGCTGGTTGTTCTTCTTCTTCAACATTAT[A/G]
ACTACCAGCAGCCGATGGAGGGCGATGGCTTGATTCTGGCTGCATAGGGGTGAAGGAGGAGGAGGAGGCTGTAAAAGAAACAAGTGATTAGACCAAATCG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.20% | 3.00% | 1.82% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.00% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 85.80% | 9.00% | 5.16% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.20% | 1.01% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 72.60% | 17.60% | 9.78% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0610766790 | T -> C | LOC_Os06g18940.1 | missense_variant ; p.Tyr598His; MODERATE | nonsynonymous_codon ; Y598H | Average:41.311; most accessible tissue: Zhenshan97 young leaf, score: 64.205 | benign  |
-0.133 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610766790 | NA | 9.21E-07 | mr1902 | Jap_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 |
| vg0610766790 | NA | 1.20E-10 | mr1087_2 | Jap_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 |
| vg0610766790 | NA | 1.78E-07 | mr1091_2 | Jap_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 |
| vg0610766790 | NA | 7.07E-06 | mr1094_2 | Jap_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 |
| vg0610766790 | NA | 2.31E-07 | mr1570_2 | Jap_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 |