| Variant ID: vg0613181958 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 13181958 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTTGACCATTTGTCTTATTCAAAAATTTTGTGCAAATGCATAAAATATAAATCATGCTTGAAGTACTTTTACTGATAAAACAACTCAACAAAATAATTA[C/T]
AATTTTTTTTAATAAGACCATTGGTCAAACGTATATTCAAGTCAACGGTGTTATCTATTAAAAAAACAGAGGTGATATCATACAATAAATTTCTGAACAA
TTGTTCAGAAATTTATTGTATGATATCACCTCTGTTTTTTTAATAGATAACACCGTTGACTTGAATATACGTTTGACCAATGGTCTTATTAAAAAAAATT[G/A]
TAATTATTTTGTTGAGTTGTTTTATCAGTAAAAGTACTTCAAGCATGATTTATATTTTATGCATTTGCACAAAATTTTTGAATAAGACAAATGGTCAAAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 1.80% | 0.51% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 93.10% | 5.40% | 1.59% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 91.80% | 5.30% | 2.87% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.00% | 16.20% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0613181958 | C -> T | LOC_Os06g22660.1 | downstream_gene_variant ; 216.0bp to feature; MODIFIER | silent_mutation | Average:49.669; most accessible tissue: Callus, score: 72.636 | N | N | N | N |
| vg0613181958 | C -> T | LOC_Os06g22670.1 | downstream_gene_variant ; 333.0bp to feature; MODIFIER | silent_mutation | Average:49.669; most accessible tissue: Callus, score: 72.636 | N | N | N | N |
| vg0613181958 | C -> T | LOC_Os06g22660.2 | downstream_gene_variant ; 216.0bp to feature; MODIFIER | silent_mutation | Average:49.669; most accessible tissue: Callus, score: 72.636 | N | N | N | N |
| vg0613181958 | C -> T | LOC_Os06g22660-LOC_Os06g22670 | intergenic_region ; MODIFIER | silent_mutation | Average:49.669; most accessible tissue: Callus, score: 72.636 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0613181958 | NA | 4.58E-06 | Grain_weight | Jap_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 |
| vg0613181958 | 4.93E-06 | NA | mr1486 | Jap_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 |
| vg0613181958 | 4.99E-06 | NA | mr1712 | Jap_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 |