Search for Variation information by Variation ID:
Detailed information for vg0432540222:
| Variant ID: vg0432540222 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 32540222 |
| Reference Allele: G | Alternative Allele: C,T |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, C: 0.23, others allele: 0.00, population size: 88. )
Flanking Sequence (100 bp) in Reference Genome:
TGACATCACGGCCAGGATGCTCTCCCGGTCGCGGTCGCAGCAGAGGGAAAGAATCCCATCGGGAATTAGTGTTGGCTCGACGGAGTCTAGGCCCAGCACC[G/C,T]
GCCGAATCACCCTCTTCACGTCCTCCTCACCCCAGTCCCAGCGCTCGCCCACATGCGTCCGCATAGGGTCGTTGGGACCAGTGTATTTCCAAGCTCCACG
Reverse complement sequence
CGTGGAGCTTGGAAATACACTGGTCCCAACGACCCTATGCGGACGCATGTGGGCGAGCGCTGGGACTGGGGTGAGGAGGACGTGAAGAGGGTGATTCGGC[C/G,A]
GGTGCTGGGCCTAGACTCCGTCGAGCCAACACTAATTCCCGATGGGATTCTTTCCCTCTGCTGCGACCGCGACCGGGAGAGCATCCTGGCCGTGATGTCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.50% | 22.10% | 0.36% | 0.00% | T: 0.04% |
| All Indica | 2759 | 73.90% | 25.50% | 0.51% | 0.00% | T: 0.07% |
| All Japonica | 1512 | 93.10% | 6.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 25.70% | 74.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 91.80% | 7.90% | 0.34% | 0.00% | NA |
| Indica II | 465 | 75.30% | 24.10% | 0.65% | 0.00% | NA |
| Indica III | 913 | 57.40% | 41.90% | 0.44% | 0.00% | T: 0.22% |
| Indica Intermediate | 786 | 78.80% | 20.60% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 81.30% | 18.50% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 78.10% | 20.80% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 18.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0432540222 | G -> C | LOC_Os04g54710.1 | missense_variant ; p.Pro212Arg; MODERATE | nonsynonymous_codon ; P212R | Average:60.085; most accessible tissue: Zhenshan97 panicle, score: 82.336 | probably damaging  |
-2.067 |
TOLERATED | 1.00 |
| vg0432540222 | G -> T | LOC_Os04g54710.1 | missense_variant ; p.Pro212Gln; MODERATE | nonsynonymous_codon ; P212Q | Average:60.085; most accessible tissue: Zhenshan97 panicle, score: 82.336 | benign |
-0.368 |
TOLERATED | 0.08 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0432540222 | 2.20E-06 | 2.20E-06 | mr1784 | 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 |
| vg0432540222 | 3.93E-10 | 2.12E-14 | mr1800 | 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 |
| vg0432540222 | 1.62E-08 | 4.10E-10 | mr1800 | 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 |
| vg0432540222 | NA | 1.79E-06 | mr1638_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 |
| vg0432540222 | NA | 2.56E-07 | mr1740_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 |
| vg0432540222 | 1.91E-06 | 3.76E-13 | mr1741_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 |
| vg0432540222 | NA | 1.99E-07 | mr1785_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 |
| vg0432540222 | 2.83E-14 | 1.33E-24 | mr1800_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 |
| vg0432540222 | 5.91E-12 | 1.27E-13 | mr1800_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 |
| vg0432540222 | NA | 1.56E-08 | mr1800_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 |