Variant ID: vg0625068802 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 25068802 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACTAATTACACAGTGTGCGTGTAAATTGCGAGATGAATCTTTTAAGCCTAATTGCACCATGATTTAACAATGTGGTGCTACAGTAAACATTTACTAATAA[C/T]
GAATTAATTAGGCTTAATAAATTTGTCTCGCAGTTTCCTAGCGAAATCTGTAATTTGTTTTGTTATTAGACTACGTTTAGTATTTCAAATGTGTGTCCGT
ACGGACACACATTTGAAATACTAAACGTAGTCTAATAACAAAACAAATTACAGATTTCGCTAGGAAACTGCGAGACAAATTTATTAAGCCTAATTAATTC[G/A]
TTATTAGTAAATGTTTACTGTAGCACCACATTGTTAAATCATGGTGCAATTAGGCTTAAAAGATTCATCTCGCAATTTACACGCACACTGTGTAATTAGT
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 | 91.00% | 9.00% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 73.10% | 26.90% | 0.00% | 0.00% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 51.80% | 48.20% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 84.60% | 15.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 90.00% | 10.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0625068802 | C -> T | LOC_Os06g41810.1 | downstream_gene_variant ; 4740.0bp to feature; MODIFIER | silent_mutation | Average:27.447; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
vg0625068802 | C -> T | LOC_Os06g41800.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.447; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0625068802 | 3.80E-06 | 2.05E-06 | mr1879_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 |