| Variant ID: vg0729156526 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 29156526 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )
TCACACGCCTTGCAAGTTACACCACTAGAGGCTCCTGGTACTGGTCAAATAACATGCTAAATGTCAGATTATAGACTGTCTCTATACATAAACTGATTTA[A/T]
GGACCCTGGTGAATTTTCATGCTTCACTTAGTATAACAAAGAATATCACATTGTAATCTCATTTACCATTTATAGTCAGTTTGTCTAAGCATTTATTTTA
TAAAATAAATGCTTAGACAAACTGACTATAAATGGTAAATGAGATTACAATGTGATATTCTTTGTTATACTAAGTGAAGCATGAAAATTCACCAGGGTCC[T/A]
TAAATCAGTTTATGTATAGAGACAGTCTATAATCTGACATTTAGCATGTTATTTGACCAGTACCAGGAGCCTCTAGTGGTGTAACTTGCAAGGCGTGTGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.30% | 19.40% | 0.28% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 1.60% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 49.50% | 49.80% | 0.73% | 0.00% | NA |
| Aus | 269 | 89.20% | 10.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 22.00% | 76.80% | 1.17% | 0.00% | NA |
| Tropical Japonica | 504 | 91.30% | 8.50% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 49.40% | 50.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 32.30% | 67.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 30.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0729156526 | A -> T | LOC_Os07g48680.1 | upstream_gene_variant ; 3092.0bp to feature; MODIFIER | silent_mutation | Average:45.68; most accessible tissue: Callus, score: 88.363 | N | N | N | N |
| vg0729156526 | A -> T | LOC_Os07g48700.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.68; most accessible tissue: Callus, score: 88.363 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0729156526 | 8.14E-12 | NA | Awn_length | 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 |
| vg0729156526 | NA | 1.60E-07 | mr1551_2 | 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 |
| vg0729156526 | NA | 4.22E-07 | mr1905_2 | 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 |