Variant ID: vg0726451328 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 26451328 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 123. )
ATTTGCTTGATTCTGACGCTGATAAATGTACTGCGGTCTGTGGATTATGTACCGTAAGGTTAGGTTAAGGCTGTGTTATACAGATACATATTTAAAGTAT[T/C]
AAACTTAGTCTAATAAAAAAACAAATTATAAAATCTACCTATAATCTGCGAGACGAATTTATTAAACCTAATTAATCTGTCATTAGCAAATGTTTACTGC
GCAGTAAACATTTGCTAATGACAGATTAATTAGGTTTAATAAATTCGTCTCGCAGATTATAGGTAGATTTTATAATTTGTTTTTTTATTAGACTAAGTTT[A/G]
ATACTTTAAATATGTATCTGTATAACACAGCCTTAACCTAACCTTACGGTACATAATCCACAGACCGCAGTACATTTATCAGCGTCAGAATCAAGCAAAT
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 | 84.10% | 13.40% | 2.54% | 0.00% | NA |
All Indica | 2759 | 73.80% | 22.30% | 3.95% | 0.00% | NA |
All Japonica | 1512 | 99.40% | 0.50% | 0.07% | 0.00% | NA |
Aus | 269 | 95.90% | 1.10% | 2.97% | 0.00% | NA |
Indica I | 595 | 38.30% | 50.60% | 11.09% | 0.00% | NA |
Indica II | 465 | 88.20% | 10.10% | 1.72% | 0.00% | NA |
Indica III | 913 | 92.40% | 7.40% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 70.40% | 25.30% | 4.33% | 0.00% | NA |
Temperate Japonica | 767 | 99.00% | 0.90% | 0.13% | 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% | 6.70% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0726451328 | T -> C | LOC_Os07g44250.1 | upstream_gene_variant ; 4805.0bp to feature; MODIFIER | silent_mutation | Average:58.958; most accessible tissue: Zhenshan97 root, score: 78.63 | N | N | N | N |
vg0726451328 | T -> C | LOC_Os07g44260.1 | upstream_gene_variant ; 858.0bp to feature; MODIFIER | silent_mutation | Average:58.958; most accessible tissue: Zhenshan97 root, score: 78.63 | N | N | N | N |
vg0726451328 | T -> C | LOC_Os07g44260-LOC_Os07g44280 | intergenic_region ; MODIFIER | silent_mutation | Average:58.958; most accessible tissue: Zhenshan97 root, score: 78.63 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0726451328 | NA | 2.61E-10 | Heading_date | 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 |
vg0726451328 | 3.31E-06 | NA | mr1065 | 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 |
vg0726451328 | 1.79E-06 | 8.66E-10 | mr1065 | 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 |
vg0726451328 | NA | 2.28E-10 | 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 |
vg0726451328 | NA | 1.41E-09 | mr1108 | 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 |
vg0726451328 | 5.06E-06 | NA | mr1200 | 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 |
vg0726451328 | NA | 4.18E-06 | mr1200 | 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 |
vg0726451328 | NA | 1.15E-09 | mr1234 | 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 |
vg0726451328 | 3.15E-06 | 1.22E-06 | mr1762 | 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 |
vg0726451328 | 2.01E-06 | 2.01E-06 | mr1762 | 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 |
vg0726451328 | NA | 6.13E-06 | mr1805 | 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 |