Search for Variation information by Variation ID:
Detailed information for vg1117137798:
| Variant ID: vg1117137798 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17137798 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACCTAGGAGTTGGCGACAACACGGATCACAACTGCTCGAAAGCTATTCGAGATTGTCGATCGATGCGCTCACACGGACGACGCACTGAGACGCAAGAAC[G/A]
ATAAGCCAAAGACGGCGGGAGAGAAGAAACCAGCCAAGGACGCACCTGAGTCAAGCAAGAAGAAGAGTCGCAAGAGTGGGAAAAGGAAAGCTCAAACGGA
Reverse complement sequence
TCCGTTTGAGCTTTCCTTTTCCCACTCTTGCGACTCTTCTTCTTGCTTGACTCAGGTGCGTCCTTGGCTGGTTTCTTCTCTCCCGCCGTCTTTGGCTTAT[C/T]
GTTCTTGCGTCTCAGTGCGTCGTCCGTGTGAGCGCATCGATCGACAATCTCGAATAGCTTTCGAGCAGTTGTGATCCGTGTTGTCGCCAACTCCTAGGTG
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 | 89.20% | 2.30% | 2.90% | 5.59% | NA |
| All Indica | 2759 | 98.10% | 0.00% | 1.67% | 0.18% | NA |
| All Japonica | 1512 | 71.60% | 6.40% | 5.49% | 16.53% | NA |
| Aus | 269 | 97.40% | 0.00% | 2.60% | 0.00% | NA |
| Indica I | 595 | 98.00% | 0.00% | 1.34% | 0.67% | NA |
| Indica II | 465 | 95.90% | 0.00% | 4.09% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 0.10% | 2.42% | 0.13% | NA |
| Temperate Japonica | 767 | 81.60% | 5.70% | 6.00% | 6.65% | NA |
| Tropical Japonica | 504 | 66.90% | 5.60% | 3.77% | 23.81% | NA |
| Japonica Intermediate | 241 | 49.40% | 10.40% | 7.47% | 32.78% | NA |
| VI/Aromatic | 96 | 85.40% | 7.30% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 93.30% | 3.30% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1117137798 | G -> A | LOC_Os11g29530.1 | missense_variant ; p.Asp236Asn; MODERATE | nonsynonymous_codon ; D236N | Average:59.844; most accessible tissue: Zhenshan97 flag leaf, score: 84.726 | benign  |
0.407 |
TOLERATED | 0.08 |
| vg1117137798 | G -> DEL | LOC_Os11g29530.1 | N | frameshift_variant | Average:59.844; most accessible tissue: Zhenshan97 flag leaf, score: 84.726 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117137798 | 3.89E-06 | 7.15E-06 | mr1928 | Jap_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 |