Search for Variation information by Variation ID:
Detailed information for vg0209778761:
| Variant ID: vg0209778761 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9778761 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 359. )
Flanking Sequence (100 bp) in Reference Genome:
CCACCCCTAGTGAATGTGATCACCGAAGGTTCCACTGACATAGTCATACCAACCGGTGCCTCAAGCGCTGCATGGTAAGTTGCTTCTGCTTCTCCAACAT[T/C]
GGTGACAGTCCGCCAAACCGTGACAGAGTCCTTTAGGTTTGGCACTGCAATTGACGGGAGGTTGAGCTGATAGATTTGCTCCATGTAGGACTCGCAGTCA
Reverse complement sequence
TGACTGCGAGTCCTACATGGAGCAAATCTATCAGCTCAACCTCCCGTCAATTGCAGTGCCAAACCTAAAGGACTCTGTCACGGTTTGGCGGACTGTCACC[A/G]
ATGTTGGAGAAGCAGAAGCAACTTACCATGCAGCGCTTGAGGCACCGGTTGGTATGACTATGTCAGTGGAACCTTCGGTGATCACATTCACTAGGGGTGG
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 | 94.80% | 4.50% | 0.72% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 84.40% | 13.60% | 1.98% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 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% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.10% | 0.30% | 2.61% | 0.00% | NA |
| Tropical Japonica | 504 | 60.50% | 37.70% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.80% | 5.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0209778761 | T -> C | LOC_Os02g17090.1 | missense_variant ; p.Asn652Asp; MODERATE | nonsynonymous_codon | Average:67.803; most accessible tissue: Zhenshan97 young leaf, score: 88.387 | possibly damaging  |
1.757 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209778761 | 3.90E-06 | 2.52E-07 | mr1398 | 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 |
| vg0209778761 | NA | 9.21E-09 | mr1422 | 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 |
| vg0209778761 | NA | 4.92E-08 | mr1696 | 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 |
| vg0209778761 | NA | 6.50E-06 | mr1218_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 |