| Variant ID: vg0522269975 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 22269975 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 277. )
CTGCATGCCGAAGCGACCCTCCCAATCAAATTTGGCAGAATCTTTCTCGATCTCCTAAAATTGATTGAAGGCTTTTGATCCACTTGATCTCCTCTTTATG[T/A]
TTTTCCTAAAATCCGAGCGAATATGCAAAACTCGGATAAAAACAGCCGAGGAAGCTCACCGGCTGGCCATCATCAGCGACTGAGATTAAATCCAGCGAAT
ATTCGCTGGATTTAATCTCAGTCGCTGATGATGGCCAGCCGGTGAGCTTCCTCGGCTGTTTTTATCCGAGTTTTGCATATTCGCTCGGATTTTAGGAAAA[A/T]
CATAAAGAGGAGATCAAGTGGATCAAAAGCCTTCAATCAATTTTAGGAGATCGAGAAAGATTCTGCCAAATTTGATTGGGAGGGTCGCTTCGGCATGCAG
| 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 | 92.50% | 6.00% | 1.46% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.50% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 79.60% | 16.20% | 4.17% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 1.50% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 83.70% | 10.20% | 6.13% | 0.00% | NA |
| Tropical Japonica | 504 | 84.70% | 13.70% | 1.59% | 0.00% | NA |
| Japonica Intermediate | 241 | 56.00% | 40.70% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 81.20% | 18.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0522269975 | T -> A | LOC_Os05g37950.1 | upstream_gene_variant ; 2968.0bp to feature; MODIFIER | silent_mutation | Average:54.291; most accessible tissue: Callus, score: 82.324 | N | N | N | N |
| vg0522269975 | T -> A | LOC_Os05g37950-LOC_Os05g37970 | intergenic_region ; MODIFIER | silent_mutation | Average:54.291; most accessible tissue: Callus, score: 82.324 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0522269975 | 4.43E-07 | 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 |
| vg0522269975 | 1.29E-08 | NA | Heading_date | 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 |
| vg0522269975 | 5.03E-06 | NA | Heading_date | 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 |
| vg0522269975 | NA | 2.74E-09 | mr1693 | 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 |