Variant ID: vg0417573231 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 17573231 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 245. )
CTGTGGACCAAAAGTGACATGGTGATGAAGAAGTGGACTTGGAGAATGTCTCATTTCCAATCAACTTATGTGATCTTCCATACATTCCTTATTCTTGGTC[T/C]
CTTTGCCTTACCCAAATAACTACCTCTGTAAACGAGAACAAGAACAGAGAAAACAAAAGGTGCAGTAATGTTTGATTAAATATATATCATATAAATCATA
TATGATTTATATGATATATATTTAATCAAACATTACTGCACCTTTTGTTTTCTCTGTTCTTGTTCTCGTTTACAGAGGTAGTTATTTGGGTAAGGCAAAG[A/G]
GACCAAGAATAAGGAATGTATGGAAGATCACATAAGTTGATTGGAAATGAGACATTCTCCAAGTCCACTTCTTCATCACCATGTCACTTTTGGTCCACAG
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 97.30% | 1.90% | 0.83% | 0.00% | NA |
All Indica | 2759 | 95.50% | 3.20% | 1.34% | 0.00% | NA |
All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 81.30% | 12.80% | 5.88% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.30% | 1.40% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 99.60% | 0.10% | 0.26% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0417573231 | T -> C | LOC_Os04g29560-LOC_Os04g29580 | intergenic_region ; MODIFIER | silent_mutation | Average:31.754; most accessible tissue: Callus, score: 65.776 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0417573231 | NA | 2.50E-06 | mr1291_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 |
vg0417573231 | NA | 4.35E-06 | mr1478_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 |
vg0417573231 | NA | 7.05E-08 | mr1502_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 |
vg0417573231 | NA | 5.99E-07 | mr1517_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 |
vg0417573231 | NA | 4.48E-08 | mr1543_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 |