Search for Variation information by Variation ID:
Detailed information for vg0136548325:
| Variant ID: vg0136548325 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36548325 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTTAAACAACAATTTATATCTTTTGAATTTTTAGGATGTGACAAACCTACCCCCCTTAAACAGAATCTCGTCCTCGAGATTCGGAAGCACTGGCGATCA[G/A,T]
ATGCGGATGAGCTGACTTCAATTCATCTTCTCGTTCCCAAGTTGATTCTTCTTCCGAGTGATTACTCCATTGGACTTTGCAAAAACGGATAACTCGATTT
Reverse complement sequence
AAATCGAGTTATCCGTTTTTGCAAAGTCCAATGGAGTAATCACTCGGAAGAAGAATCAACTTGGGAACGAGAAGATGAATTGAAGTCAGCTCATCCGCAT[C/T,A]
TGATCGCCAGTGCTTCCGAATCTCGAGGACGAGATTCTGTTTAAGGGGGGTAGGTTTGTCACATCCTAAAAATTCAAAAGATATAAATTGTTGTTTAAAT
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 | 36.50% | 2.50% | 21.29% | 39.67% | T: 0.02% |
| All Indica | 2759 | 7.70% | 0.00% | 28.78% | 63.50% | NA |
| All Japonica | 1512 | 86.70% | 7.80% | 3.97% | 1.46% | T: 0.07% |
| Aus | 269 | 17.50% | 0.00% | 53.90% | 28.62% | NA |
| Indica I | 595 | 8.60% | 0.00% | 18.49% | 72.94% | NA |
| Indica II | 465 | 5.60% | 0.00% | 18.28% | 76.13% | NA |
| Indica III | 913 | 5.10% | 0.00% | 43.15% | 51.70% | NA |
| Indica Intermediate | 786 | 11.30% | 0.00% | 26.08% | 62.60% | NA |
| Temperate Japonica | 767 | 81.90% | 11.60% | 5.61% | 0.91% | NA |
| Tropical Japonica | 504 | 94.60% | 1.40% | 1.59% | 2.18% | T: 0.20% |
| Japonica Intermediate | 241 | 85.50% | 9.10% | 3.73% | 1.66% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 7.78% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136548325 | G -> T | LOC_Os01g63080.1 | missense_variant ; p.Leu1654Met; MODERATE | nonsynonymous_codon ; L1654M | Average:7.173; most accessible tissue: Callus, score: 23.183 | probably damaging  |
2.427 |
DELETERIOUS | 0.00 |
| vg0136548325 | G -> A | LOC_Os01g63080.1 | synonymous_variant ; p.Leu1654Leu; LOW | synonymous_codon | Average:7.173; most accessible tissue: Callus, score: 23.183 | N | N | N | N |
| vg0136548325 | G -> DEL | LOC_Os01g63080.1 | N | frameshift_variant | Average:7.173; most accessible tissue: Callus, score: 23.183 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136548325 | 1.19E-11 | 2.50E-16 | Awn_length | Jap_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |