Variant ID: vg0301192756 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 1192756 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 241. )
TACTATGACGGCGGTCTCGCTGGTGTGATAGCGTTATTTGGTCATGCCAGTCTCGCTAGCGTGGCAACGTTATTTAGTCACGCCGCTCTTACTGATGTGG[C/T]
TGGATAAAACTGTCACGTCCATTGCATATGGCATGTTAGTGTTGTTTTATCACGTCAGGCGGGATAGTGTGACCAAAAGGTTCAAATTTTGAGAATAAGT
ACTTATTCTCAAAATTTGAACCTTTTGGTCACACTATCCCGCCTGACGTGATAAAACAACACTAACATGCCATATGCAATGGACGTGACAGTTTTATCCA[G/A]
CCACATCAGTAAGAGCGGCGTGACTAAATAACGTTGCCACGCTAGCGAGACTGGCATGACCAAATAACGCTATCACACCAGCGAGACCGCCGTCATAGTA
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.50% | 8.50% | 0.04% | 0.00% | NA |
All Indica | 2759 | 87.00% | 12.90% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 89.20% | 10.80% | 0.00% | 0.00% | NA |
Indica I | 595 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 66.00% | 34.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 97.30% | 2.60% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 83.80% | 16.00% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 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 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 91.10% | 8.90% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0301192756 | C -> T | LOC_Os03g02960.1 | upstream_gene_variant ; 1499.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0301192756 | C -> T | LOC_Os03g02970.1 | downstream_gene_variant ; 2319.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0301192756 | C -> T | LOC_Os03g02939-LOC_Os03g02960 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0301192756 | NA | 1.06E-06 | mr1319 | 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 |
vg0301192756 | NA | 1.27E-08 | mr1332 | 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 |
vg0301192756 | NA | 8.45E-07 | mr1944 | 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 |
vg0301192756 | 2.70E-06 | 8.40E-07 | mr1977 | 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 |
vg0301192756 | 7.07E-06 | 1.54E-06 | mr1977 | 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 |