Search for Variation information by Variation ID:
Detailed information for vg1115982226:
| Variant ID: vg1115982226 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 15982226 |
| Reference Allele: G | Alternative Allele: A,T,GAA |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 103. )
Flanking Sequence (100 bp) in Reference Genome:
GATCAAATTTGATGATTCCAAGAGGCCAATGAAGGTTGATGGTAATCCTTTTCCTATCAATATGGTACACACAGCTGGCCGAACAGCCGACGGAGGACGT[G/A,T,GAA]
CGAGAGGTTTTCAGGTGAATTCGGCTAAAATTATAAACAAGTATCAAAGGAAGTATGACAAGCAACAGGAGAGGCGTTATGAAGAAGATAATGGTGGTTT
Reverse complement sequence
AAACCACCATTATCTTCTTCATAACGCCTCTCCTGTTGCTTGTCATACTTCCTTTGATACTTGTTTATAATTTTAGCCGAATTCACCTGAAAACCTCTCG[C/T,A,TTC]
ACGTCCTCCGTCGGCTGTTCGGCCAGCTGTGTGTACCATATTGATAGGAAAAGGATTACCATCAACCTTCATTGGCCTCTTGGAATCATCAAATTTGATC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.40% | 11.00% | 10.14% | 1.12% | GAA: 0.32% |
| All Indica | 2759 | 68.00% | 15.40% | 14.32% | 1.74% | GAA: 0.54% |
| All Japonica | 1512 | 99.50% | 0.20% | 0.13% | 0.13% | NA |
| Aus | 269 | 43.50% | 27.90% | 28.25% | 0.37% | NA |
| Indica I | 595 | 88.70% | 2.40% | 8.24% | 0.67% | NA |
| Indica II | 465 | 42.60% | 37.00% | 19.14% | 1.08% | GAA: 0.22% |
| Indica III | 913 | 68.50% | 11.80% | 15.66% | 2.52% | GAA: 1.53% |
| Indica Intermediate | 786 | 66.80% | 16.70% | 14.50% | 2.04% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 14.40% | 5.56% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115982226 | G -> GAA | LOC_Os11g27760.1 | frameshift_variant ; p.Ala564fs; HIGH | frameshift_variant | Average:21.951; most accessible tissue: Callus, score: 34.91 | N | N | N | N |
| vg1115982226 | G -> A | LOC_Os11g27760.1 | missense_variant ; p.Ala564Thr; MODERATE | nonsynonymous_codon ; A564T | Average:21.951; most accessible tissue: Callus, score: 34.91 | benign  |
0.567 |
TOLERATED | 0.33 |
| vg1115982226 | G -> DEL | LOC_Os11g27760.1 | N | frameshift_variant | Average:21.951; most accessible tissue: Callus, score: 34.91 | N | N | N | N |
| vg1115982226 | G -> T | LOC_Os11g27760.1 | missense_variant ; p.Ala564Ser; MODERATE | N | Average:21.951; most accessible tissue: Callus, score: 34.91 | N | N | N | N |
| vg1115982226 | G -> T | LOC_Os11g27750.1 | upstream_gene_variant ; 4218.0bp to feature; MODIFIER | N | Average:21.951; most accessible tissue: Callus, score: 34.91 | N | N | N | N |
| vg1115982226 | G -> T | LOC_Os11g27770.1 | downstream_gene_variant ; 4818.0bp to feature; MODIFIER | N | Average:21.951; most accessible tissue: Callus, score: 34.91 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1115982226 | NA | 7.63E-06 | mr1011 | 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 |
| vg1115982226 | 4.59E-06 | 4.58E-06 | mr1012 | 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 |
| vg1115982226 | NA | 8.26E-06 | mr1012 | 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 |