Variant ID: vg0802250534 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 2250534 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.23, others allele: 0.00, population size: 99. )
GAGACAAAAGGGGTTTATATAGATTCGGGCAGCTGAGATGCGTAGTACCCTACTCCTGTGTTTGGGATTATGGATGAGTGTTACAAAGATTCCTTCCCTC[C/T]
AGAGAGCTCTTTCGCCCTACTTCTCCTAGAGTTCAGGTTTTCTTAGAGTCGTCCGTTTTTTTCTCGGTGGGCAAGGTTCTCCTTTTATAGTTCAAGGGGA
TCCCCTTGAACTATAAAAGGAGAACCTTGCCCACCGAGAAAAAAACGGACGACTCTAAGAAAACCTGAACTCTAGGAGAAGTAGGGCGAAAGAGCTCTCT[G/A]
GAGGGAAGGAATCTTTGTAACACTCATCCATAATCCCAAACACAGGAGTAGGGTACTACGCATCTCAGCTGCCCGAATCTATATAAACCCCTTTTGTCTC
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 | 89.90% | 9.90% | 0.13% | 0.00% | NA |
All Indica | 2759 | 87.20% | 12.80% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 92.50% | 7.20% | 0.33% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
Indica II | 465 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 78.60% | 21.40% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 87.40% | 12.50% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 93.40% | 5.40% | 1.24% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 92.20% | 6.70% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0802250534 | C -> T | LOC_Os08g04530-LOC_Os08g04540 | intergenic_region ; MODIFIER | silent_mutation | Average:39.751; most accessible tissue: Minghui63 root, score: 55.188 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0802250534 | NA | 2.30E-06 | mr1425 | 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 |
vg0802250534 | 5.08E-06 | 5.08E-06 | mr1524 | 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 |
vg0802250534 | 2.49E-06 | 2.14E-06 | mr1751 | Jap_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 |
vg0802250534 | NA | 5.53E-06 | mr1780 | 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 |
vg0802250534 | NA | 8.43E-06 | mr1790 | 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 |