Variant ID: vg0914433559 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 14433559 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 259. )
TTTATGGCTGCACCATTTAATTTTCCACGTCATATGTTTGATCTGTACCACCATATTCTATCACATAATTAAAGAGGACAAGAACAAAAGTACGTGTCAT[A/T]
TGCATTTATCCATTCATGACTCAATTCTTTATCCTTCCACATCATCAACTCCACCTCCAACTCATTCTATCCCTAAGAATAAATGAAGAGATAAGAAAGC
GCTTTCTTATCTCTTCATTTATTCTTAGGGATAGAATGAGTTGGAGGTGGAGTTGATGATGTGGAAGGATAAAGAATTGAGTCATGAATGGATAAATGCA[T/A]
ATGACACGTACTTTTGTTCTTGTCCTCTTTAATTATGTGATAGAATATGGTGGTACAGATCAAACATATGACGTGGAAAATTAAATGGTGCAGCCATAAA
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 | 88.30% | 3.90% | 7.83% | 0.00% | NA |
All Indica | 2759 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
All Japonica | 1512 | 65.60% | 11.20% | 23.15% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 99.40% | 0.30% | 0.38% | 0.00% | NA |
Temperate Japonica | 767 | 90.90% | 2.00% | 7.17% | 0.00% | NA |
Tropical Japonica | 504 | 33.50% | 25.00% | 41.47% | 0.00% | NA |
Japonica Intermediate | 241 | 52.30% | 12.00% | 35.68% | 0.00% | NA |
VI/Aromatic | 96 | 89.60% | 5.20% | 5.21% | 0.00% | NA |
Intermediate | 90 | 84.40% | 5.60% | 10.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0914433559 | A -> T | LOC_Os09g24290.1 | upstream_gene_variant ; 812.0bp to feature; MODIFIER | silent_mutation | Average:34.123; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
vg0914433559 | A -> T | LOC_Os09g24280-LOC_Os09g24290 | intergenic_region ; MODIFIER | silent_mutation | Average:34.123; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0914433559 | NA | 8.59E-06 | mr1502 | 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 |
vg0914433559 | 4.34E-06 | 8.58E-08 | mr1543 | 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 |
vg0914433559 | NA | 5.88E-08 | mr1543 | Jap_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 |
vg0914433559 | NA | 8.12E-09 | mr1449_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 |