Variant ID: vg0715862869 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 15862869 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )
TAAACACAGAGAGAAGCAATAAAGTTGTCATCTACTTTGAGAGTTCTTCTATTTGTGTTTCACCGGGTTTCGGCGGTCTAACCGGCATCTCACCGGCGGT[C/T]
AGACTGGCGACCTACTGGCGGTCAAACCGACTAAGGCGAGGCGGTCAGACCGGTGGCGGCGACAGCGACTTCAGACGCGGCAGACGATCTTCAGGCGGTT
AACCGCCTGAAGATCGTCTGCCGCGTCTGAAGTCGCTGTCGCCGCCACCGGTCTGACCGCCTCGCCTTAGTCGGTTTGACCGCCAGTAGGTCGCCAGTCT[G/A]
ACCGCCGGTGAGATGCCGGTTAGACCGCCGAAACCCGGTGAAACACAAATAGAAGAACTCTCAAAGTAGATGACAACTTTATTGCTTCTCTCTGTGTTTA
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 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
All Indica | 2759 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 84.50% | 15.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 92.20% | 7.80% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 4.40% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0715862869 | C -> T | LOC_Os07g27290.1 | synonymous_variant ; p.Val184Val; LOW | synonymous_codon | Average:45.21; most accessible tissue: Zhenshan97 root, score: 57.64 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0715862869 | 1.06E-07 | 1.56E-11 | mr1059 | 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 |
vg0715862869 | 8.27E-06 | 1.68E-09 | mr1167 | 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 |
vg0715862869 | 1.47E-06 | 3.23E-10 | mr1535 | 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 |
vg0715862869 | 1.66E-07 | 1.11E-11 | mr1675 | 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 |
vg0715862869 | NA | 2.08E-08 | mr1950 | 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 |