Search for Variation information by Variation ID:
Detailed information for vg0519167166:
| Variant ID: vg0519167166 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 19167166 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )
Flanking Sequence (100 bp) in Reference Genome:
GACAACAATGTTGAAGGTCCAGCTATTTGGAGCAATGCCTTTCTTGGCCATGTCAGTGAAAAGTTTGACAACAGACAGCCATCTGTGCTCATCGCAAAGC[T/C]
TCCTCATCACCGTGTTATAATTGACAACATTGGCATCCCACCCAAGCTCTGCGCTGCACTCCAAGAGGCGTTTTGCAGCCCATGCAGTTGAGCTACGACA
Reverse complement sequence
TGTCGTAGCTCAACTGCATGGGCTGCAAAACGCCTCTTGGAGTGCAGCGCAGAGCTTGGGTGGGATGCCAATGTTGTCAATTATAACACGGTGATGAGGA[A/G]
GCTTTGCGATGAGCACAGATGGCTGTCTGTTGTCAAACTTTTCACTGACATGGCCAAGAAAGGCATTGCTCCAAATAGCTGGACCTTCAACATTGTTGTC
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 | 70.00% | 29.90% | 0.00% | 0.06% | NA |
| All Indica | 2759 | 99.20% | 0.80% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 15.50% | 84.50% | 0.00% | 0.07% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.10% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 5.30% | 94.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 31.20% | 68.70% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 14.90% | 85.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 28.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0519167166 | T -> DEL | LOC_Os05g32730.1 | N | frameshift_variant | Average:62.449; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |
| vg0519167166 | T -> C | LOC_Os05g32730.1 | missense_variant ; p.Lys357Arg; MODERATE | nonsynonymous_codon ; K357R | Average:62.449; most accessible tissue: Minghui63 flag leaf, score: 80.786 | benign  |
-0.424 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0519167166 | NA | 1.57E-09 | mr1277 | 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 |
| vg0519167166 | 6.66E-06 | NA | mr1301 | 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 |
| vg0519167166 | 1.20E-07 | NA | mr1410 | 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 |
| vg0519167166 | NA | 1.49E-07 | mr1676 | 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 |
| vg0519167166 | 1.80E-07 | NA | mr1410_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 |
| vg0519167166 | NA | 1.03E-06 | mr1629_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 |
| vg0519167166 | NA | 2.38E-07 | mr1676_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 |