| Variant ID: vg0629496844 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29496844 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 117. )
TGTTATAAGGTGAGAGTAGTTTAATTGGTTAGATTTTTGTTGTGAAATCAGCTCATCTGAATTCAAGTTCTAAACTTGACATGAATGCTTATATTTATAA[C/T]
TAATTATTCTTTTAGTGGTAGATGACATACTCGTGAGAGTAAGGCGTCCGTAATGATTTCATCAATTTCAAGATATGTCAGTCTAGTCTTCCGGAGATGT
ACATCTCCGGAAGACTAGACTGACATATCTTGAAATTGATGAAATCATTACGGACGCCTTACTCTCACGAGTATGTCATCTACCACTAAAAGAATAATTA[G/A]
TTATAAATATAAGCATTCATGTCAAGTTTAGAACTTGAATTCAGATGAGCTGATTTCACAACAAAAATCTAACCAATTAAACTACTCTCACCTTATAACA
| 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 | 87.10% | 12.40% | 0.49% | 0.00% | NA |
| All Indica | 2759 | 79.30% | 20.00% | 0.69% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 1.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 54.60% | 43.70% | 1.68% | 0.00% | NA |
| Indica II | 465 | 72.30% | 27.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 95.50% | 4.30% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 83.20% | 16.20% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 15.60% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629496844 | C -> T | LOC_Os06g48730.1 | upstream_gene_variant ; 606.0bp to feature; MODIFIER | silent_mutation | Average:38.596; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0629496844 | C -> T | LOC_Os06g48740.1 | upstream_gene_variant ; 4907.0bp to feature; MODIFIER | silent_mutation | Average:38.596; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0629496844 | C -> T | LOC_Os06g48720-LOC_Os06g48730 | intergenic_region ; MODIFIER | silent_mutation | Average:38.596; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0629496844 | NA | 4.47E-10 | Heading_date | 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 |
| vg0629496844 | NA | 3.77E-07 | mr1242 | 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 |
| vg0629496844 | NA | 9.24E-06 | mr1123_2 | 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 |
| vg0629496844 | NA | 7.26E-06 | mr1125_2 | 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 |
| vg0629496844 | NA | 1.39E-09 | mr1242_2 | Ind_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 |
| vg0629496844 | NA | 6.89E-07 | mr1870_2 | 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 |