| Variant ID: vg0120478712 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 20478712 |
| 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: 107. )
GTGCTGCCCTGTGAGAGACAAAGTAGAGAGAGGAAGAGGGGAAGAGGTGTATGACAGGTGGGTCCGATATTTTTTAATAAATAAAATGCTGACTAGATTG[C/T]
CACGTGTACACCACGTAGGATAAAACTGCTCTGGATTAGGTCAAGGGAGGTAATTCGTCCGGTATTGAAAGTTGAGGGTGAGCAATGTCTGGTTTTTTTG
CAAAAAAACCAGACATTGCTCACCCTCAACTTTCAATACCGGACGAATTACCTCCCTTGACCTAATCCAGAGCAGTTTTATCCTACGTGGTGTACACGTG[G/A]
CAATCTAGTCAGCATTTTATTTATTAAAAAATATCGGACCCACCTGTCATACACCTCTTCCCCTCTTCCTCTCTCTACTTTGTCTCTCACAGGGCAGCAC
| 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 | 80.20% | 19.70% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 66.90% | 32.90% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 14.50% | 85.20% | 0.34% | 0.00% | NA |
| Indica II | 465 | 71.20% | 28.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 70.70% | 28.90% | 0.38% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0120478712 | C -> T | LOC_Os01g36800.1 | downstream_gene_variant ; 3847.0bp to feature; MODIFIER | silent_mutation | Average:79.413; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0120478712 | C -> T | LOC_Os01g36810.1 | downstream_gene_variant ; 87.0bp to feature; MODIFIER | silent_mutation | Average:79.413; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0120478712 | C -> T | LOC_Os01g36820.1 | downstream_gene_variant ; 1288.0bp to feature; MODIFIER | silent_mutation | Average:79.413; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0120478712 | C -> T | LOC_Os01g36810-LOC_Os01g36820 | intergenic_region ; MODIFIER | silent_mutation | Average:79.413; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0120478712 | NA | 7.52E-43 | mr1067 | 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 |
| vg0120478712 | NA | 1.91E-14 | mr1067 | 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 |
| vg0120478712 | NA | 3.35E-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 |
| vg0120478712 | NA | 8.61E-09 | mr1069 | 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 |
| vg0120478712 | NA | 2.61E-26 | mr1072 | 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 |
| vg0120478712 | NA | 2.11E-10 | mr1072 | 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 |
| vg0120478712 | NA | 1.91E-09 | mr1075 | 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 |
| vg0120478712 | NA | 1.75E-22 | mr1077 | 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 |
| vg0120478712 | NA | 9.15E-09 | mr1077 | 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 |
| vg0120478712 | NA | 1.37E-06 | mr1080 | 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 |
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