Variant ID: vg0518191135 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 18191135 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )
TGGAATCAGTAACTGAGAATTCTCAAGATCCTTATTTTGCTTGAGGATGAGAGGCAACGAAGTCAACTGCCGTTTTGATGGAGTCAATCTTCTCTGCCTC[G/A]
TTATCTGGGATCTCGAAGCCAAATTCTTCCTCAAAGGCCATGACAATCTCAACTGTATCCAAGCTATCAAGTCCGAGGTCCTTCTGGAAATGAGCATTTG
CAAATGCTCATTTCCAGAAGGACCTCGGACTTGATAGCTTGGATACAGTTGAGATTGTCATGGCCTTTGAGGAAGAATTTGGCTTCGAGATCCCAGATAA[C/T]
GAGGCAGAGAAGATTGACTCCATCAAAACGGCAGTTGACTTCGTTGCCTCTCATCCTCAAGCAAAATAAGGATCTTGAGAATTCTCAGTTACTGATTCCA
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 97.30% | 1.60% | 1.06% | 0.00% | NA |
All Indica | 2759 | 95.50% | 2.70% | 1.78% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 82.50% | 10.60% | 6.89% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.70% | 1.30% | 1.02% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 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 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0518191135 | G -> A | LOC_Os05g31290.1 | synonymous_variant ; p.Asn107Asn; LOW | synonymous_codon | Average:63.376; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0518191135 | NA | 1.58E-07 | mr1709 | 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 |
vg0518191135 | 1.92E-07 | NA | mr1980 | 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 |
vg0518191135 | 7.85E-06 | 7.85E-06 | mr1821_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 |