Search for Variation information by Variation ID:
Detailed information for vg0622592636:
| Variant ID: vg0622592636 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22592636 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGGCGAGATGGTTCTATCTTTAGATAGAGAACTCGGATCCTGTCCTTGTTGTCCCTGAAGAACAACCAGACAAGATCCCAGAGTGGACCGCCAAACCCG[C/A,T]
CCTGACTCCCTCCCTCCAGTCTTTCATCGACATCATCGATGACCTCCGAATACGGGGGTTGTCGGGGTATGAAGTCGCTGCCGACTTCGTAGGTAGGCGG
Reverse complement sequence
CCGCCTACCTACGAAGTCGGCAGCGACTTCATACCCCGACAACCCCCGTATTCGGAGGTCATCGATGATGTCGATGAAAGACTGGAGGGAGGGAGTCAGG[G/T,A]
CGGGTTTGGCGGTCCACTCTGGGATCTTGTCTGGTTGTTCTTCAGGGACAACAAGGACAGGATCCGAGTTCTCTATCTAAAGATAGAACCATCTCGCCCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.60% | 29.20% | 5.56% | 16.57% | T: 0.02% |
| All Indica | 2759 | 71.80% | 20.20% | 7.14% | 0.91% | T: 0.04% |
| All Japonica | 1512 | 3.70% | 50.90% | 2.51% | 42.92% | NA |
| Aus | 269 | 78.80% | 4.80% | 5.58% | 10.78% | NA |
| Indica I | 595 | 55.00% | 39.20% | 5.55% | 0.34% | NA |
| Indica II | 465 | 77.00% | 18.70% | 4.09% | 0.22% | NA |
| Indica III | 913 | 77.20% | 8.90% | 12.49% | 1.42% | NA |
| Indica Intermediate | 786 | 75.10% | 19.70% | 3.94% | 1.15% | T: 0.13% |
| Temperate Japonica | 767 | 1.00% | 76.40% | 1.56% | 20.99% | NA |
| Tropical Japonica | 504 | 7.10% | 18.50% | 3.57% | 70.83% | NA |
| Japonica Intermediate | 241 | 5.00% | 37.30% | 3.32% | 54.36% | NA |
| VI/Aromatic | 96 | 15.60% | 6.20% | 7.29% | 70.83% | NA |
| Intermediate | 90 | 40.00% | 40.00% | 6.67% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622592636 | C -> T | LOC_Os06g38140.1 | missense_variant ; p.Ala87Val; MODERATE | nonsynonymous_codon ; A87V | Average:18.131; most accessible tissue: Minghui63 young leaf, score: 24.836 | benign  |
0.56 |
TOLERATED | 0.08 |
| vg0622592636 | C -> A | LOC_Os06g38140.1 | missense_variant ; p.Ala87Asp; MODERATE | nonsynonymous_codon ; A87D | Average:18.131; most accessible tissue: Minghui63 young leaf, score: 24.836 | benign |
0.633 |
TOLERATED | 0.06 |
| vg0622592636 | C -> DEL | LOC_Os06g38140.1 | N | frameshift_variant | Average:18.131; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622592636 | 9.74E-06 | NA | Awn_length | All | Not | 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 |
| vg0622592636 | 2.17E-06 | 8.70E-06 | mr1800 | 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 |