Search for Variation information by Variation ID:
Detailed information for vg1126117539:
| Variant ID: vg1126117539 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26117539 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, T: 0.32, others allele: 0.00, population size: 53. )
Flanking Sequence (100 bp) in Reference Genome:
TGAACAAGATCACGCCAATCATCTACGAAAAGTAATGGAAAGGTTGCGTGAACACCAGCTCTTCACCAATTACTCGAAGTGTGAGTTCTGGTTGGATAAA[T/G]
TAGCCTTCCTTGGCCATGTCATTTCCACCAAAGGTGTTGAAGTAGACCCCAGTAAGGTTGAGACCGTCCTCGCCTGGAACGCACCAAAGACGGTGTCTGA
Reverse complement sequence
TCAGACACCGTCTTTGGTGCGTTCCAGGCGAGGACGGTCTCAACCTTACTGGGGTCTACTTCAACACCTTTGGTGGAAATGACATGGCCAAGGAAGGCTA[A/C]
TTTATCCAACCAGAACTCACACTTCGAGTAATTGGTGAAGAGCTGGTGTTCACGCAACCTTTCCATTACTTTTCGTAGATGATTGGCGTGATCTTGTTCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.10% | 25.50% | 1.12% | 25.29% | NA |
| All Indica | 2759 | 64.20% | 9.80% | 0.87% | 25.19% | NA |
| All Japonica | 1512 | 16.10% | 59.00% | 1.06% | 23.81% | NA |
| Aus | 269 | 69.10% | 4.50% | 2.23% | 24.16% | NA |
| Indica I | 595 | 39.70% | 19.30% | 1.18% | 39.83% | NA |
| Indica II | 465 | 77.40% | 4.30% | 0.65% | 17.63% | NA |
| Indica III | 913 | 72.80% | 2.50% | 0.55% | 24.10% | NA |
| Indica Intermediate | 786 | 64.80% | 14.20% | 1.15% | 19.85% | NA |
| Temperate Japonica | 767 | 3.90% | 85.80% | 0.78% | 9.52% | NA |
| Tropical Japonica | 504 | 31.90% | 21.80% | 1.59% | 44.64% | NA |
| Japonica Intermediate | 241 | 22.00% | 51.50% | 0.83% | 25.73% | NA |
| VI/Aromatic | 96 | 27.10% | 11.50% | 3.12% | 58.33% | NA |
| Intermediate | 90 | 50.00% | 24.40% | 4.44% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126117539 | T -> DEL | LOC_Os11g43290.1 | N | frameshift_variant | Average:38.404; most accessible tissue: Minghui63 flag leaf, score: 78.782 | N | N | N | N |
| vg1126117539 | T -> G | LOC_Os11g43290.1 | missense_variant ; p.Leu498Val; MODERATE | nonsynonymous_codon ; L498V | Average:38.404; most accessible tissue: Minghui63 flag leaf, score: 78.782 | benign  |
-0.512 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126117539 | NA | 9.14E-07 | mr1252 | 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 |
| vg1126117539 | NA | 1.90E-06 | mr1359 | 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 |
| vg1126117539 | 3.06E-07 | 3.06E-07 | mr1499 | 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 |
| vg1126117539 | NA | 2.69E-07 | mr1576 | 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 |
| vg1126117539 | NA | 1.82E-06 | mr1808 | 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 |
| vg1126117539 | NA | 9.08E-07 | mr1826 | 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 |