Search for Variation information by Variation ID:
Detailed information for vg1126117503:
| Variant ID: vg1126117503 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26117503 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.56, A: 0.41, others allele: 0.00, population size: 41. )
Flanking Sequence (100 bp) in Reference Genome:
GGTCTTCATCGACGACATTCTGATTTACTCAAGGGATGAACAAGATCACGCCAATCATCTACGAAAAGTAATGGAAAGGTTGCGTGAACACCAGCTCTTC[A/G]
CCAATTACTCGAAGTGTGAGTTCTGGTTGGATAAATTAGCCTTCCTTGGCCATGTCATTTCCACCAAAGGTGTTGAAGTAGACCCCAGTAAGGTTGAGAC
Reverse complement sequence
GTCTCAACCTTACTGGGGTCTACTTCAACACCTTTGGTGGAAATGACATGGCCAAGGAAGGCTAATTTATCCAACCAGAACTCACACTTCGAGTAATTGG[T/C]
GAAGAGCTGGTGTTCACGCAACCTTTCCATTACTTTTCGTAGATGATTGGCGTGATCTTGTTCATCCCTTGAGTAAATCAGAATGTCGTCGATGAAGACC
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 | 46.80% | 25.70% | 2.01% | 25.48% | NA |
| All Indica | 2759 | 62.90% | 9.20% | 2.17% | 25.73% | NA |
| All Japonica | 1512 | 14.90% | 60.10% | 1.32% | 23.68% | NA |
| Aus | 269 | 66.90% | 7.10% | 2.60% | 23.42% | NA |
| Indica I | 595 | 50.80% | 8.70% | 3.70% | 36.81% | NA |
| Indica II | 465 | 76.30% | 4.70% | 2.15% | 16.77% | NA |
| Indica III | 913 | 58.40% | 11.30% | 1.86% | 28.48% | NA |
| Indica Intermediate | 786 | 69.50% | 9.70% | 1.40% | 19.47% | NA |
| Temperate Japonica | 767 | 3.80% | 85.70% | 0.91% | 9.65% | NA |
| Tropical Japonica | 504 | 30.00% | 23.80% | 1.39% | 44.84% | NA |
| Japonica Intermediate | 241 | 19.10% | 54.40% | 2.49% | 24.07% | NA |
| VI/Aromatic | 96 | 26.00% | 12.50% | 5.21% | 56.25% | NA |
| Intermediate | 90 | 48.90% | 26.70% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1126117503 | A -> DEL | LOC_Os11g43290.1 | N | frameshift_variant | Average:38.222; most accessible tissue: Minghui63 flag leaf, score: 81.052 | N | N | N | N |
| vg1126117503 | A -> G | LOC_Os11g43290.1 | missense_variant ; p.Thr486Ala; MODERATE | nonsynonymous_codon ; T486A | Average:38.222; most accessible tissue: Minghui63 flag leaf, score: 81.052 | possibly damaging  |
-1.662 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126117503 | NA | 2.00E-06 | 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 |
| vg1126117503 | NA | 3.82E-07 | 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 |
| vg1126117503 | NA | 3.45E-06 | mr1826 | 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 |
| vg1126117503 | 6.17E-06 | 4.40E-06 | mr1631_2 | 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 |