| Variant ID: vg0700638475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 638475 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.18, others allele: 0.00, population size: 191. )
GCGCATTTTATATATTGAAAGTTACTGGAAATTCAACGAATTACTTTCACCCTCTCAAAATGTAAACCTTTCGAAAAAACTACTCCTTCCAACTACTTTT[A/G]
ATAGCCATTCTACTTAATTAATTCTACTTATCATCTATTTAAATATGCTACGAGTCATTACTCGTAAATAAGCGATTCATTAATATTTACATTTCTCAAT
ATTGAGAAATGTAAATATTAATGAATCGCTTATTTACGAGTAATGACTCGTAGCATATTTAAATAGATGATAAGTAGAATTAATTAAGTAGAATGGCTAT[T/C]
AAAAGTAGTTGGAAGGAGTAGTTTTTTCGAAAGGTTTACATTTTGAGAGGGTGAAAGTAATTCGTTGAATTTCCAGTAACTTTCAATATATAAAATGCGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.60% | 49.30% | 1.06% | 0.00% | NA |
| All Indica | 2759 | 24.70% | 73.60% | 1.70% | 0.00% | NA |
| All Japonica | 1512 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 4.80% | 94.10% | 1.12% | 0.00% | NA |
| Indica I | 595 | 3.50% | 95.60% | 0.84% | 0.00% | NA |
| Indica II | 465 | 82.40% | 16.10% | 1.51% | 0.00% | NA |
| Indica III | 913 | 6.20% | 93.00% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 28.10% | 68.30% | 3.56% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 32.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0700638475 | A -> G | LOC_Os07g02060.1 | upstream_gene_variant ; 4159.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700638475 | A -> G | LOC_Os07g02060-LOC_Os07g02070 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0700638475 | NA | 1.71E-10 | Grain_width | 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 |
| vg0700638475 | NA | 1.09E-09 | mr1005 | 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 |
| vg0700638475 | NA | 3.22E-09 | mr1050 | 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 |
| vg0700638475 | NA | 1.93E-14 | mr1059 | 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 |
| vg0700638475 | NA | 4.07E-14 | mr1069 | 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 |
| vg0700638475 | NA | 2.51E-06 | mr1074 | 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 |
| vg0700638475 | NA | 4.80E-07 | mr1094 | 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 |
| vg0700638475 | NA | 1.68E-06 | mr1098 | 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 |
| vg0700638475 | NA | 2.15E-17 | mr1133 | 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 |
| vg0700638475 | NA | 4.73E-15 | mr1143 | 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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