Search for Variation information by Variation ID:
Detailed information for vg1124757031:
| Variant ID: vg1124757031 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24757031 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.57, A: 0.42, others allele: 0.00, population size: 99. )
Flanking Sequence (100 bp) in Reference Genome:
CCGGAGCTGGACGGCGGCAGCGCGGCGGCGATGGCGCAGCACCTGCTGGTGGCGGCGGACAGGTACGACATGGAGAGGCTGAAGAAGGTGTGCGAGGACA[G/A]
GATGGTCAGGCACCTCGACGTCGGCACGGCGGCGACGTCGCTGGCGTTGGCCGAGCAGCACGATTGCCCTGAGCTCAAGAAGGCCATCCTGAGGTTCATG
Reverse complement sequence
CATGAACCTCAGGATGGCCTTCTTGAGCTCAGGGCAATCGTGCTGCTCGGCCAACGCCAGCGACGTCGCCGCCGTGCCGACGTCGAGGTGCCTGACCATC[C/T]
TGTCCTCGCACACCTTCTTCAGCCTCTCCATGTCGTACCTGTCCGCCGCCACCAGCAGGTGCTGCGCCATCGCCGCCGCGCTGCCGCCGTCCAGCTCCGG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.50% | 30.00% | 0.08% | 0.40% | NA |
| All Indica | 2759 | 86.50% | 12.90% | 0.07% | 0.58% | NA |
| All Japonica | 1512 | 36.20% | 63.60% | 0.00% | 0.20% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 75.10% | 23.70% | 0.17% | 1.01% | NA |
| Indica II | 465 | 91.80% | 7.30% | 0.00% | 0.86% | NA |
| Indica III | 913 | 91.30% | 8.10% | 0.11% | 0.44% | NA |
| Indica Intermediate | 786 | 86.30% | 13.50% | 0.00% | 0.25% | NA |
| Temperate Japonica | 767 | 15.40% | 84.50% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 59.90% | 39.90% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 52.70% | 46.90% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 30.20% | 69.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 31.10% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124757031 | G -> A | LOC_Os11g41300.1 | missense_variant ; p.Arg289Lys; MODERATE | nonsynonymous_codon ; R289K | Average:76.558; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | benign  |
-0.239 |
TOLERATED | 1.00 |
| vg1124757031 | G -> DEL | LOC_Os11g41300.1 | N | frameshift_variant | Average:76.558; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124757031 | NA | 5.79E-07 | mr1543 | 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 |
| vg1124757031 | NA | 2.46E-08 | mr1871 | 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 |
| vg1124757031 | NA | 1.57E-08 | mr1871_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 |