| Variant ID: vg0133381779 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 33381779 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 122. )
AGTAAAAAATTGAACCTAAACGATAATTATGTTCGATTTTTAAAATCTCAATGACAATAAAGAGAAGAAACAGTGGACGGGCCGTAGAGGAGTATAATGG[C/T]
AACATTTGACGGGACATCTAGAAATTATAAAAACGAAACCCATCGTGACAATAAACTCTAAAAACTATAAAATCCAATTTTTAAAGGTTCCAAGAAGAAT
ATTCTTCTTGGAACCTTTAAAAATTGGATTTTATAGTTTTTAGAGTTTATTGTCACGATGGGTTTCGTTTTTATAATTTCTAGATGTCCCGTCAAATGTT[G/A]
CCATTATACTCCTCTACGGCCCGTCCACTGTTTCTTCTCTTTATTGTCATTGAGATTTTAAAAATCGAACATAATTATCGTTTAGGTTCAATTTTTTACT
| 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 | 66.70% | 32.40% | 0.51% | 0.36% | NA |
| All Indica | 2759 | 43.40% | 55.10% | 0.87% | 0.62% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 23.50% | 74.30% | 2.02% | 0.17% | NA |
| Indica II | 465 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 23.20% | 75.60% | 0.33% | 0.88% | NA |
| Indica Intermediate | 786 | 52.50% | 45.30% | 1.15% | 1.02% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0133381779 | C -> T | LOC_Os01g57730.1 | downstream_gene_variant ; 550.0bp to feature; MODIFIER | silent_mutation | Average:44.431; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |
| vg0133381779 | C -> T | LOC_Os01g57720-LOC_Os01g57730 | intergenic_region ; MODIFIER | silent_mutation | Average:44.431; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |
| vg0133381779 | C -> DEL | N | N | silent_mutation | Average:44.431; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0133381779 | 1.73E-06 | NA | Plant_height | 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 |
| vg0133381779 | 6.43E-08 | 4.08E-24 | Plant_height | Ind_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 |
| vg0133381779 | NA | 7.34E-06 | mr1014 | Ind_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 |
| vg0133381779 | NA | 4.15E-10 | mr1277 | 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 |
| vg0133381779 | NA | 1.17E-07 | mr1277 | Ind_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 |
| vg0133381779 | NA | 8.87E-07 | mr1352 | Ind_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 |
| vg0133381779 | NA | 2.46E-06 | mr1627 | Ind_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 |
| vg0133381779 | NA | 6.33E-06 | mr1636 | Ind_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 |
| vg0133381779 | NA | 5.08E-06 | mr1839 | Ind_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 |
| vg0133381779 | NA | 1.62E-07 | mr1045_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 |
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