Search for Variation information by Variation ID:
Detailed information for vg1117136142:
| Variant ID: vg1117136142 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17136142 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 73. )
Flanking Sequence (100 bp) in Reference Genome:
GGAGAATGGAACATCGACGATATCCAAGCCCAAGAAGGATCCTAATGCGGCCAAATCTTGTCCTTCCGACGAGAATCACGAGCCGACAAGAACCACTTCT[G/A]
AGGCAACAAGGTCTTGGTGTCCTATCCACAAAACCAGGAAGCACACCTTGCAAGCTTGCTGGGTTTTTCTCGACGTACAAGCTGAGATCCGTGCCTGCAA
Reverse complement sequence
TTGCAGGCACGGATCTCAGCTTGTACGTCGAGAAAAACCCAGCAAGCTTGCAAGGTGTGCTTCCTGGTTTTGTGGATAGGACACCAAGACCTTGTTGCCT[C/T]
AGAAGTGGTTCTTGTCGGCTCGTGATTCTCGTCGGAAGGACAAGATTTGGCCGCATTAGGATCCTTCTTGGGCTTGGATATCGTCGATGTTCCATTCTCC
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 | 44.80% | 32.20% | 5.86% | 17.20% | NA |
| All Indica | 2759 | 40.00% | 47.20% | 4.06% | 8.70% | NA |
| All Japonica | 1512 | 52.80% | 8.00% | 5.95% | 33.27% | NA |
| Aus | 269 | 56.10% | 21.20% | 20.45% | 2.23% | NA |
| Indica I | 595 | 16.00% | 77.10% | 1.01% | 5.88% | NA |
| Indica II | 465 | 46.50% | 28.40% | 9.25% | 15.91% | NA |
| Indica III | 913 | 50.40% | 40.50% | 2.19% | 6.90% | NA |
| Indica Intermediate | 786 | 42.40% | 43.50% | 5.47% | 8.65% | NA |
| Temperate Japonica | 767 | 84.00% | 2.00% | 0.52% | 13.56% | NA |
| Tropical Japonica | 504 | 21.80% | 16.50% | 14.88% | 46.83% | NA |
| Japonica Intermediate | 241 | 18.30% | 9.50% | 4.56% | 67.63% | NA |
| VI/Aromatic | 96 | 29.20% | 3.10% | 16.67% | 51.04% | NA |
| Intermediate | 90 | 38.90% | 40.00% | 4.44% | 16.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117136142 | G -> A | LOC_Os11g29530.1 | missense_variant ; p.Glu77Lys; MODERATE | nonsynonymous_codon ; E77K | Average:57.503; most accessible tissue: Minghui63 young leaf, score: 74.007 | benign  |
0.235 |
TOLERATED | 0.09 |
| vg1117136142 | G -> DEL | LOC_Os11g29530.1 | N | frameshift_variant | Average:57.503; most accessible tissue: Minghui63 young leaf, score: 74.007 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117136142 | NA | 8.70E-06 | mr1352 | 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 |
| vg1117136142 | 2.02E-06 | 2.02E-06 | mr1428 | 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 |
| vg1117136142 | NA | 6.46E-06 | mr1958 | 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 |