Search for Variation information by Variation ID:
Detailed information for vg0117732560:
| Variant ID: vg0117732560 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 17732560 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
TTGAACACCCACTTGCACCCCACAGGTTTACACCCATAGGGTCGCTCTGTCACCTCCCAAGTCCCGTTAGCGATAATGGAGTCCATTTCACTACGGACAG[C/T]
CTCCTTCCAGTAGTCTACATCAGAAGATGCATATGCTTCTGAAATTGACTTAGGAGTGTCATCCACGAGGTACACAGTGAAATCATCACCAAAGGACTTA
Reverse complement sequence
TAAGTCCTTTGGTGATGATTTCACTGTGTACCTCGTGGATGACACTCCTAAGTCAATTTCAGAAGCATATGCATCTTCTGATGTAGACTACTGGAAGGAG[G/A]
CTGTCCGTAGTGAAATGGACTCCATTATCGCTAACGGGACTTGGGAGGTGACAGAGCGACCCTATGGGTGTAAACCTGTGGGGTGCAAGTGGGTGTTCAA
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 | 93.00% | 6.70% | 0.30% | 0.00% | NA |
| All Indica | 2759 | 92.30% | 7.30% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 60.60% | 37.90% | 1.49% | 0.00% | NA |
| Indica I | 595 | 92.90% | 6.40% | 0.67% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.00% | 11.70% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 92.90% | 6.70% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0117732560 | C -> T | LOC_Os01g32320.1 | missense_variant ; p.Ala541Thr; MODERATE | nonsynonymous_codon ; A541T | Average:23.772; most accessible tissue: Minghui63 panicle, score: 29.741 | benign  |
0.877 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0117732560 | NA | 7.96E-06 | mr1042 | 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 |
| vg0117732560 | NA | 2.31E-06 | mr1042 | 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 |
| vg0117732560 | NA | 2.69E-06 | mr1043 | 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 |
| vg0117732560 | NA | 1.77E-06 | mr1043 | 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 |
| vg0117732560 | NA | 7.90E-07 | mr1912 | 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 |
| vg0117732560 | 4.71E-06 | 2.17E-07 | mr1912 | 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 |