| Variant ID: vg0628528239 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 28528239 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, T: 0.36, others allele: 0.00, population size: 77. )
TTCGGTTACGCGGAGTGGAGATCGTGCGGGCGCCCTGATCAAGCGACCTATCTCTATATAAACCGAGCCGCCACCTTCACGCAAAATACACGAAATCAAT[C/T]
TAGGGTTTGCCTCCTCCTCTGTGTTGCGCCGTCGCTCGTGGACTACTCCATCCCACTCGCTAGCGTGCACCGGTGATCGGGAGAGCAGGTCTCCGGAACC
GGTTCCGGAGACCTGCTCTCCCGATCACCGGTGCACGCTAGCGAGTGGGATGGAGTAGTCCACGAGCGACGGCGCAACACAGAGGAGGAGGCAAACCCTA[G/A]
ATTGATTTCGTGTATTTTGCGTGAAGGTGGCGGCTCGGTTTATATAGAGATAGGTCGCTTGATCAGGGCGCCCGCACGATCTCCACTCCGCGTAACCGAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.40% | 33.00% | 0.02% | 5.59% | NA |
| All Indica | 2759 | 95.10% | 2.90% | 0.00% | 2.07% | NA |
| All Japonica | 1512 | 4.80% | 95.10% | 0.00% | 0.07% | NA |
| Aus | 269 | 24.20% | 3.70% | 0.00% | 72.12% | NA |
| Indica I | 595 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.60% | 1.10% | 0.00% | 1.29% | NA |
| Indica III | 913 | 95.40% | 0.50% | 0.00% | 4.05% | NA |
| Indica Intermediate | 786 | 95.80% | 2.40% | 0.00% | 1.78% | NA |
| Temperate Japonica | 767 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 7.50% | 92.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 91.70% | 2.10% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 57.80% | 34.40% | 1.11% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0628528239 | C -> T | LOC_Os06g47030.1 | downstream_gene_variant ; 4024.0bp to feature; MODIFIER | silent_mutation | Average:50.124; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg0628528239 | C -> T | LOC_Os06g47040.1 | downstream_gene_variant ; 2411.0bp to feature; MODIFIER | silent_mutation | Average:50.124; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg0628528239 | C -> T | LOC_Os06g47060.1 | downstream_gene_variant ; 3371.0bp to feature; MODIFIER | silent_mutation | Average:50.124; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg0628528239 | C -> T | LOC_Os06g47050.1 | intron_variant ; MODIFIER | silent_mutation | Average:50.124; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| vg0628528239 | C -> DEL | N | N | silent_mutation | Average:50.124; most accessible tissue: Zhenshan97 panicle, score: 76.605 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0628528239 | NA | 1.51E-24 | mr1251 | 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 |
| vg0628528239 | NA | 1.78E-19 | mr1253 | 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 |
| vg0628528239 | NA | 4.28E-08 | mr1610 | 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 |
| vg0628528239 | NA | 1.22E-28 | mr1638 | 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 |
| vg0628528239 | NA | 3.25E-37 | mr1828 | 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 |
| vg0628528239 | NA | 2.43E-17 | mr1913 | 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 |
| vg0628528239 | NA | 2.22E-06 | mr1105_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 |
| vg0628528239 | NA | 1.35E-13 | mr1151_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 |
| vg0628528239 | NA | 1.15E-08 | mr1198_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 |
| vg0628528239 | NA | 8.10E-07 | mr1275_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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