Variant ID: vg0428010540 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 28010540 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.12, others allele: 0.00, population size: 103. )
TCATAAGAATCAATCTTTTTAAAGAGAAAGGTAGGAGCTTTGTCGATCAAGAAATAAACAAAAACAATAAATTTGATTTCCACGATAATTAGGAAGAGGT[T/C]
ATTTAGACCCTCTTTGTTTGGGCTTAGGTTTATTGGTTTAGATTTTTAAGTTAGCTTATTGGCTTATATGATTTATAAGCTGGTAGATTTAATGTTCTAA
TTAGAACATTAAATCTACCAGCTTATAAATCATATAAGCCAATAAGCTAACTTAAAAATCTAAACCAATAAACCTAAGCCCAAACAAAGAGGGTCTAAAT[A/G]
ACCTCTTCCTAATTATCGTGGAAATCAAATTTATTGTTTTTGTTTATTTCTTGATCGACAAAGCTCCTACCTTTCTCTTTAAAAAGATTGATTCTTATGA
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 | 58.60% | 41.40% | 0.02% | 0.00% | NA |
All Indica | 2759 | 92.80% | 7.20% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
Aus | 269 | 59.90% | 40.10% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 95.70% | 4.10% | 0.22% | 0.00% | NA |
Indica III | 913 | 88.10% | 11.90% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 93.60% | 6.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 40.00% | 60.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0428010540 | T -> C | LOC_Os04g47170.1 | upstream_gene_variant ; 3179.0bp to feature; MODIFIER | silent_mutation | Average:38.244; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
vg0428010540 | T -> C | LOC_Os04g47160-LOC_Os04g47170 | intergenic_region ; MODIFIER | silent_mutation | Average:38.244; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0428010540 | NA | 4.24E-09 | mr1663 | 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 |
vg0428010540 | NA | 2.00E-06 | mr1137_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 |
vg0428010540 | NA | 2.11E-41 | mr1145_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 |
vg0428010540 | NA | 6.61E-36 | mr1181_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 |
vg0428010540 | 6.64E-06 | NA | mr1241_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 |
vg0428010540 | NA | 2.75E-07 | mr1804_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 |