| Variant ID: vg0518201525 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 18201525 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 254. )
CAGGTGCGTGAACCCTAAATGCTGGCGATGAGCGTGCTGGAGGAGACGAAGGGAGGCGAGAGCGTGCTGCGGAGAGGAAGGGAGCAGGCAAGCATGCACG[C/T]
GAGTACTGCAACCTTTACTTGAGAGCCGAGAACGGGCGGTGAGGCAAGAGAAATGAGGCGCCGCGCAATTAATGGCGAGCAGAACGGGAGCGAGCGCTAG
CTAGCGCTCGCTCCCGTTCTGCTCGCCATTAATTGCGCGGCGCCTCATTTCTCTTGCCTCACCGCCCGTTCTCGGCTCTCAAGTAAAGGTTGCAGTACTC[G/A]
CGTGCATGCTTGCCTGCTCCCTTCCTCTCCGCAGCACGCTCTCGCCTCCCTTCGTCTCCTCCAGCACGCTCATCGCCAGCATTTAGGGTTCACGCACCTG
| 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 | 94.20% | 5.70% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 1.40% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 19.00% | 81.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 1.30% | 0.25% | 0.00% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0518201525 | C -> T | LOC_Os05g31310.1 | upstream_gene_variant ; 297.0bp to feature; MODIFIER | silent_mutation | Average:66.448; most accessible tissue: Zhenshan97 young leaf, score: 83.831 | N | N | N | N |
| vg0518201525 | C -> T | LOC_Os05g31320.1 | upstream_gene_variant ; 1549.0bp to feature; MODIFIER | silent_mutation | Average:66.448; most accessible tissue: Zhenshan97 young leaf, score: 83.831 | N | N | N | N |
| vg0518201525 | C -> T | LOC_Os05g31300.1 | downstream_gene_variant ; 2109.0bp to feature; MODIFIER | silent_mutation | Average:66.448; most accessible tissue: Zhenshan97 young leaf, score: 83.831 | N | N | N | N |
| vg0518201525 | C -> T | LOC_Os05g31310-LOC_Os05g31320 | intergenic_region ; MODIFIER | silent_mutation | Average:66.448; most accessible tissue: Zhenshan97 young leaf, score: 83.831 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0518201525 | NA | 5.35E-06 | mr1006 | 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 |
| vg0518201525 | NA | 4.79E-06 | mr1052 | 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 |
| vg0518201525 | NA | 4.27E-32 | mr1098 | 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 |
| vg0518201525 | NA | 1.24E-27 | mr1099 | 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 |
| vg0518201525 | NA | 2.61E-27 | mr1101 | 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 |
| vg0518201525 | NA | 5.90E-21 | mr1113 | 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 |
| vg0518201525 | NA | 4.72E-24 | mr1114 | 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 |
| vg0518201525 | NA | 3.98E-20 | mr1116 | 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 |
| vg0518201525 | 3.37E-06 | 1.01E-26 | mr1117 | 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 |
| vg0518201525 | NA | 2.21E-22 | mr1119 | 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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