Variant ID: vg0234310744 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 34310744 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 232. )
GCAACCTTTATAGCCTCTAATGCTTGAAGGCAGCCGATTACTCCTGGAACTAACAAACAAAAATGTAGACATTGGATCATTCATATAGACAATATGGATG[G/A]
GATATTAGAAAACCGGCCTCTACATCCACGACAAGTACATTTACATGTACCTATGAAGATAATATACCTATACCTATGGAATTCCTCTACTTATTCTACT
AGTAGAATAAGTAGAGGAATTCCATAGGTATAGGTATATTATCTTCATAGGTACATGTAAATGTACTTGTCGTGGATGTAGAGGCCGGTTTTCTAATATC[C/T]
CATCCATATTGTCTATATGAATGATCCAATGTCTACATTTTTGTTTGTTAGTTCCAGGAGTAATCGGCTGCCTTCAAGCATTAGAGGCTATAAAGGTTGC
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 | 51.70% | 47.80% | 0.42% | 0.02% | NA |
All Indica | 2759 | 28.30% | 71.10% | 0.54% | 0.04% | NA |
All Japonica | 1512 | 94.00% | 5.90% | 0.13% | 0.00% | NA |
Aus | 269 | 60.20% | 39.80% | 0.00% | 0.00% | NA |
Indica I | 595 | 44.40% | 54.60% | 1.01% | 0.00% | NA |
Indica II | 465 | 13.80% | 86.00% | 0.22% | 0.00% | NA |
Indica III | 913 | 21.00% | 78.60% | 0.22% | 0.11% | NA |
Indica Intermediate | 786 | 33.10% | 66.20% | 0.76% | 0.00% | NA |
Temperate Japonica | 767 | 97.50% | 2.30% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 88.70% | 11.10% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 34.40% | 65.60% | 0.00% | 0.00% | NA |
Intermediate | 90 | 54.40% | 42.20% | 3.33% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0234310744 | G -> A | LOC_Os02g56040.1 | upstream_gene_variant ; 3015.0bp to feature; MODIFIER | silent_mutation | Average:43.899; most accessible tissue: Callus, score: 83.15 | N | N | N | N |
vg0234310744 | G -> A | LOC_Os02g56060.1 | upstream_gene_variant ; 1962.0bp to feature; MODIFIER | silent_mutation | Average:43.899; most accessible tissue: Callus, score: 83.15 | N | N | N | N |
vg0234310744 | G -> A | LOC_Os02g56050.1 | intron_variant ; MODIFIER | silent_mutation | Average:43.899; most accessible tissue: Callus, score: 83.15 | N | N | N | N |
vg0234310744 | G -> DEL | N | N | silent_mutation | Average:43.899; most accessible tissue: Callus, score: 83.15 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0234310744 | NA | 7.61E-06 | mr1041_2 | 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 |
vg0234310744 | NA | 3.50E-06 | mr1294_2 | 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 |
vg0234310744 | NA | 3.84E-08 | mr1418_2 | 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 |
vg0234310744 | NA | 6.39E-06 | mr1420_2 | 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 |
vg0234310744 | NA | 4.23E-07 | mr1488_2 | 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 |
vg0234310744 | NA | 2.22E-06 | mr1497_2 | 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 |
vg0234310744 | NA | 1.16E-09 | mr1506_2 | 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 |
vg0234310744 | NA | 3.00E-07 | mr1604_2 | 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 |
vg0234310744 | NA | 5.14E-10 | mr1659_2 | 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 |
vg0234310744 | NA | 7.06E-06 | mr1779_2 | 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 |
vg0234310744 | NA | 1.73E-06 | mr1992_2 | 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 |