Variant ID: vg0726174758 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 26174758 |
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: 111. )
ACAGAGGCTCATTCAGATTTGTAGTATTAAAATATATCTAGATTCATAGGGTCTGTTTGGTACAGCTCCAACTCCTAAATTTAACTCCAGGAGTTGAGTC[T/C]
GGAGTGGAGTTGTGGAGCTGTCTAAACCCAGCTCCACAACTCTAGTTCATTTTGTGAGAGCTCCACTACCAGTTTTGGTGGAGCTGAAACTGTTTGGCTG
CAGCCAAACAGTTTCAGCTCCACCAAAACTGGTAGTGGAGCTCTCACAAAATGAACTAGAGTTGTGGAGCTGGGTTTAGACAGCTCCACAACTCCACTCC[A/G]
GACTCAACTCCTGGAGTTAAATTTAGGAGTTGGAGCTGTACCAAACAGACCCTATGAATCTAGATATATTTTAATACTACAAATCTGAATGAGCCTCTGT
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 | 90.90% | 9.00% | 0.11% | 0.00% | NA |
All Indica | 2759 | 86.70% | 13.20% | 0.18% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 78.40% | 21.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
Indica II | 465 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
Indica III | 913 | 76.90% | 23.00% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 84.90% | 14.60% | 0.51% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 96.70% | 3.30% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0726174758 | T -> C | LOC_Os07g43750.1 | upstream_gene_variant ; 1820.0bp to feature; MODIFIER | silent_mutation | Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 | N | N | N | N |
vg0726174758 | T -> C | LOC_Os07g43730.1 | downstream_gene_variant ; 2202.0bp to feature; MODIFIER | silent_mutation | Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 | N | N | N | N |
vg0726174758 | T -> C | LOC_Os07g43740.1 | downstream_gene_variant ; 372.0bp to feature; MODIFIER | silent_mutation | Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 | N | N | N | N |
vg0726174758 | T -> C | LOC_Os07g43740-LOC_Os07g43750 | intergenic_region ; MODIFIER | silent_mutation | Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0726174758 | NA | 8.42E-06 | mr1107 | 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 |
vg0726174758 | NA | 4.11E-07 | mr1226 | 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 |
vg0726174758 | NA | 1.88E-06 | mr1144_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 |
vg0726174758 | NA | 5.85E-08 | mr1155_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 |
vg0726174758 | NA | 4.60E-06 | mr1168_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 |
vg0726174758 | 4.17E-06 | NA | mr1198_2 | 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 |
vg0726174758 | NA | 2.87E-06 | mr1620_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 |