| Variant ID: vg1128198374 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28198374 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, C: 0.18, others allele: 0.00, population size: 168. )
AAATTTGCTCCCTTCCTTTCGCCATTATTCCCCTTGCCTTCGCCGCTTGCGCCCTAACTCTTTCTCTGCTGCGCCCTACCTTCGCCACACGCGCTCGTTC[C/T]
CAATCATCCCTTCCTCCGGCGTCATGGCACGGGGCTCCGCCCTGCTCGACGGTAGCGTACTACCGCCTTCTCGCATCGTGAGCGAGAGGCAGGCCGGGCT
AGCCCGGCCTGCCTCTCGCTCACGATGCGAGAAGGCGGTAGTACGCTACCGTCGAGCAGGGCGGAGCCCCGTGCCATGACGCCGGAGGAAGGGATGATTG[G/A]
GAACGAGCGCGTGTGGCGAAGGTAGGGCGCAGCAGAGAAAGAGTTAGGGCGCAAGCGGCGAAGGCAAGGGGAATAATGGCGAAAGGAAGGGAGCAAATTT
| 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 | 27.90% | 9.60% | 50.78% | 11.74% | NA |
| All Indica | 2759 | 12.30% | 12.10% | 70.21% | 5.40% | NA |
| All Japonica | 1512 | 50.40% | 2.60% | 20.70% | 26.26% | NA |
| Aus | 269 | 65.10% | 5.90% | 28.25% | 0.74% | NA |
| Indica I | 595 | 6.10% | 10.10% | 79.16% | 4.71% | NA |
| Indica II | 465 | 6.50% | 11.40% | 63.44% | 18.71% | NA |
| Indica III | 913 | 17.10% | 12.30% | 70.65% | 0.00% | NA |
| Indica Intermediate | 786 | 14.80% | 14.00% | 66.92% | 4.33% | NA |
| Temperate Japonica | 767 | 36.50% | 2.00% | 17.73% | 43.81% | NA |
| Tropical Japonica | 504 | 67.10% | 4.20% | 24.21% | 4.56% | NA |
| Japonica Intermediate | 241 | 59.80% | 1.70% | 22.82% | 15.77% | NA |
| VI/Aromatic | 96 | 13.50% | 55.20% | 31.25% | 0.00% | NA |
| Intermediate | 90 | 34.40% | 8.90% | 48.89% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1128198374 | C -> T | LOC_Os11g46910.1 | upstream_gene_variant ; 1772.0bp to feature; MODIFIER | silent_mutation | Average:16.183; most accessible tissue: Callus, score: 27.094 | N | N | N | N |
| vg1128198374 | C -> T | LOC_Os11g46920.1 | upstream_gene_variant ; 24.0bp to feature; MODIFIER | silent_mutation | Average:16.183; most accessible tissue: Callus, score: 27.094 | N | N | N | N |
| vg1128198374 | C -> T | LOC_Os11g46930.1 | downstream_gene_variant ; 3815.0bp to feature; MODIFIER | silent_mutation | Average:16.183; most accessible tissue: Callus, score: 27.094 | N | N | N | N |
| vg1128198374 | C -> T | LOC_Os11g46910-LOC_Os11g46920 | intergenic_region ; MODIFIER | silent_mutation | Average:16.183; most accessible tissue: Callus, score: 27.094 | N | N | N | N |
| vg1128198374 | C -> DEL | N | N | silent_mutation | Average:16.183; most accessible tissue: Callus, score: 27.094 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128198374 | 2.60E-07 | NA | Spikelet_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 |
| vg1128198374 | NA | 3.65E-08 | mr1260 | 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 |
| vg1128198374 | NA | 8.65E-07 | mr1321 | 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 |
| vg1128198374 | NA | 2.05E-07 | mr1321_2 | 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 |