Variant ID: vg0113853307 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 13853307 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 115. )
AAAAACCAACACAAGATAATGAAAACATAATTATTGAATTCTATTTGTGAATCTCTACCCGAAGTTGGCAAAAAGTTGTATAACCATTGACTCAAGTTTA[C/T]
GACATACATTATTAATTAGCATGATATTCTCATCAGACCTTTGTAATTGGGCACAACACCGGAGCCAATACGTTATACGTTGCCCAGAAAAGTACCTGCA
TGCAGGTACTTTTCTGGGCAACGTATAACGTATTGGCTCCGGTGTTGTGCCCAATTACAAAGGTCTGATGAGAATATCATGCTAATTAATAATGTATGTC[G/A]
TAAACTTGAGTCAATGGTTATACAACTTTTTGCCAACTTCGGGTAGAGATTCACAAATAGAATTCAATAATTATGTTTTCATTATCTTGTGTTGGTTTTT
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 | 68.80% | 31.10% | 0.08% | 0.00% | NA |
All Indica | 2759 | 60.50% | 39.30% | 0.14% | 0.00% | NA |
All Japonica | 1512 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Aus | 269 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 67.60% | 32.40% | 0.00% | 0.00% | NA |
Indica II | 465 | 91.00% | 9.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 42.40% | 57.30% | 0.33% | 0.00% | NA |
Indica Intermediate | 786 | 58.30% | 41.60% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 29.20% | 70.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 74.40% | 25.60% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0113853307 | C -> T | LOC_Os01g24570.1 | upstream_gene_variant ; 4271.0bp to feature; MODIFIER | silent_mutation | Average:53.228; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
vg0113853307 | C -> T | LOC_Os01g24590.1 | downstream_gene_variant ; 4294.0bp to feature; MODIFIER | silent_mutation | Average:53.228; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
vg0113853307 | C -> T | LOC_Os01g24570-LOC_Os01g24590 | intergenic_region ; MODIFIER | silent_mutation | Average:53.228; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0113853307 | NA | 5.54E-06 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0113853307 | NA | 6.70E-06 | mr1277_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 |
vg0113853307 | NA | 4.14E-09 | mr1519_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 |
vg0113853307 | NA | 7.47E-06 | mr1587_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 |
vg0113853307 | NA | 5.86E-06 | mr1792_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 |
vg0113853307 | NA | 5.24E-06 | mr1803_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 |
vg0113853307 | NA | 1.02E-06 | mr1874_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 |