Variant ID: vg0630863586 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 30863586 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, T: 0.08, others allele: 0.00, population size: 209. )
CAAAAGATTCGTCTCGCAGTTTACAGTCCAAATATGTAATTTATTTTGTTATTAGTCTACGTTTAATACTTCAAATGTGTGTCCGTATACGTCAAAAAAA[A/T]
TTTTGACGCCGAACTAAACACGGCTTTTGTTTAAAATGTGCTTGCATGATATTGGCTGAAAATAGATTTTTTTATCATCTCCTATATATATACCTTACAT
ATGTAAGGTATATATATAGGAGATGATAAAAAAATCTATTTTCAGCCAATATCATGCAAGCACATTTTAAACAAAAGCCGTGTTTAGTTCGGCGTCAAAA[T/A]
TTTTTTTGACGTATACGGACACACATTTGAAGTATTAAACGTAGACTAATAACAAAATAAATTACATATTTGGACTGTAAACTGCGAGACGAATCTTTTG
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 89.60% | 10.40% | 0.02% | 0.00% | NA |
All Indica | 2759 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 83.10% | 16.80% | 0.07% | 0.00% | NA |
Aus | 269 | 51.30% | 48.70% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 54.40% | 45.40% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 92.10% | 7.90% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 54.20% | 45.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 87.80% | 12.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0630863586 | A -> T | LOC_Os06g51000.1 | upstream_gene_variant ; 2427.0bp to feature; MODIFIER | silent_mutation | Average:42.702; most accessible tissue: Zhenshan97 root, score: 77.09 | N | N | N | N |
vg0630863586 | A -> T | LOC_Os06g50990.1 | downstream_gene_variant ; 4123.0bp to feature; MODIFIER | silent_mutation | Average:42.702; most accessible tissue: Zhenshan97 root, score: 77.09 | N | N | N | N |
vg0630863586 | A -> T | LOC_Os06g50990-LOC_Os06g51000 | intergenic_region ; MODIFIER | silent_mutation | Average:42.702; most accessible tissue: Zhenshan97 root, score: 77.09 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0630863586 | 4.72E-06 | NA | mr1362_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 |
vg0630863586 | NA | 4.15E-06 | mr1762_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 |
vg0630863586 | 2.26E-06 | NA | mr1836_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 |