Variant ID: vg0313045453 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 13045453 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 182. )
TAGGAATAGAAAAATCGTAGGAATATGATAGGAATGTATGTGTAAAACGGAGGATTGGAAAACACAGGAATTCTGTAGATAGGATTGGTAAACATGTGTT[T/C]
GGATAGGCAGAGGAAAAACATAGGAAATAGAAAAAATGAGGTAGGAGTGGATGGAAATTTTCCTTTGTTTCTCTATTGTTTCCACAGGAAAGGAATTTTT
AAAAATTCCTTTCCTGTGGAAACAATAGAGAAACAAAGGAAAATTTCCATCCACTCCTACCTCATTTTTTCTATTTCCTATGTTTTTCCTCTGCCTATCC[A/G]
AACACATGTTTACCAATCCTATCTACAGAATTCCTGTGTTTTCCAATCCTCCGTTTTACACATACATTCCTATCATATTCCTACGATTTTTCTATTCCTA
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 | 87.60% | 12.30% | 0.06% | 0.00% | NA |
All Indica | 2759 | 84.80% | 15.20% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 45.70% | 53.90% | 0.37% | 0.00% | NA |
Indica I | 595 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
Indica II | 465 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 77.10% | 22.90% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 84.70% | 15.30% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 87.80% | 10.00% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0313045453 | T -> C | LOC_Os03g22620.1 | 5_prime_UTR_variant ; 2565.0bp to feature; MODIFIER | silent_mutation | Average:32.979; most accessible tissue: Callus, score: 51.351 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0313045453 | NA | 1.01E-06 | mr1004 | 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 |
vg0313045453 | NA | 2.88E-06 | mr1208_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 |
vg0313045453 | NA | 8.14E-07 | 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 |
vg0313045453 | NA | 7.06E-06 | mr1762_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 |
vg0313045453 | 4.08E-06 | NA | mr1800_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 |