Variant ID: vg0528941797 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 28941797 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )
CATGTTGGTAGTTCCTCTAACTTATTTTCATGTCTGTTCAGATCCTTTTCATGAAGTGAGAAGAAAGCGTGACAAGAAAAAGGAGGTAAGCATATGAACT[C/A]
TGAATTCTATATGCTGCCAGTTCTTAAGGAAATTCACTGTTTGGTTTTCCTCCCTGTTTATTTTGTGTGAGTTTTCCATCTCAATGCGAATATAGTGTCA
TGACACTATATTCGCATTGAGATGGAAAACTCACACAAAATAAACAGGGAGGAAAACCAAACAGTGAATTTCCTTAAGAACTGGCAGCATATAGAATTCA[G/T]
AGTTCATATGCTTACCTCCTTTTTCTTGTCACGCTTTCTTCTCACTTCATGAAAAGGATCTGAACAGACATGAAAATAAGTTAGAGGAACTACCAACATG
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 85.90% | 14.10% | 0.00% | 0.00% | NA |
All Indica | 2759 | 77.20% | 22.80% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Aus | 269 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
Indica I | 595 | 37.60% | 62.40% | 0.00% | 0.00% | NA |
Indica II | 465 | 77.40% | 22.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 81.00% | 19.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 82.20% | 17.80% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0528941797 | C -> A | LOC_Os05g50480.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.37; most accessible tissue: Callus, score: 81.147 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0528941797 | 2.16E-06 | NA | mr1065 | 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 |
vg0528941797 | NA | 7.82E-10 | mr1065 | 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 |
vg0528941797 | NA | 7.77E-11 | mr1067 | 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 |
vg0528941797 | 8.09E-06 | NA | mr1110 | 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 |
vg0528941797 | NA | 3.02E-07 | mr1221 | 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 |
vg0528941797 | NA | 2.04E-08 | mr1234 | 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 |
vg0528941797 | NA | 5.24E-07 | mr1850 | 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 |
vg0528941797 | NA | 1.39E-10 | mr1067_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 |
vg0528941797 | NA | 1.06E-10 | mr1234_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 |