Variant ID: vg1213914027 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 13914027 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.13, others allele: 0.00, population size: 250. )
TCAGGATGGCGTTTAACGACGATGAGAAGCCTGCTACTACTCCAATTCCGAATGGAGGTATCGTCTTAATTCCATCAGCCTTCCATTGATGCATTACATA[C/T]
TGGAATACATACCGTTTGCCGCAATTTCGAAATGATCCTGCATTGAGGCGGATTCAATACATGTATATATGATGTGCAGGGAGCAAACAGGGCCTCGTGA
TCACGAGGCCCTGTTTGCTCCCTGCACATCATATATACATGTATTGAATCCGCCTCAATGCAGGATCATTTCGAAATTGCGGCAAACGGTATGTATTCCA[G/A]
TATGTAATGCATCAATGGAAGGCTGATGGAATTAAGACGATACCTCCATTCGGAATTGGAGTAGTAGCAGGCTTCTCATCGTCGTTAAACGCCATCCTGA
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 | 50.00% | 49.80% | 0.15% | 0.00% | NA |
All Indica | 2759 | 50.30% | 49.50% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 60.30% | 39.70% | 0.07% | 0.00% | NA |
Aus | 269 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 44.20% | 55.80% | 0.00% | 0.00% | NA |
Indica II | 465 | 56.60% | 43.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 46.80% | 53.10% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 55.50% | 44.30% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 88.30% | 11.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 16.90% | 82.90% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 61.80% | 38.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 5.20% | 94.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 57.80% | 38.90% | 3.33% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1213914027 | C -> T | LOC_Os12g24400.1 | upstream_gene_variant ; 3384.0bp to feature; MODIFIER | silent_mutation | Average:75.171; most accessible tissue: Callus, score: 90.748 | N | N | N | N |
vg1213914027 | C -> T | LOC_Os12g24390.1 | intron_variant ; MODIFIER | silent_mutation | Average:75.171; most accessible tissue: Callus, score: 90.748 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1213914027 | NA | 1.76E-07 | mr1190 | 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 |
vg1213914027 | NA | 1.39E-06 | mr1207 | 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 |
vg1213914027 | NA | 3.52E-06 | mr1209 | 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 |
vg1213914027 | NA | 2.44E-06 | mr1308 | 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 |
vg1213914027 | NA | 2.47E-06 | mr1460 | 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 |
vg1213914027 | NA | 6.37E-06 | mr1606 | 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 |
vg1213914027 | NA | 2.44E-06 | mr1633 | 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 |
vg1213914027 | NA | 9.68E-06 | mr1700 | 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 |
vg1213914027 | NA | 5.54E-08 | mr1706 | 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 |
vg1213914027 | NA | 1.10E-08 | mr1866 | 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 |