Variant ID: vg1018076166 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 18076166 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTCTCAATGTGATTATTCCTACTTTATTTACTCTTGATACATTTATAGCCTGCTTTTTACAAATTTCGATGTAATGATTATTTAGAAATAAATTTATATT[T/C]
GAACAAATAAGAGTGGCTAAAAATAAAACTTATTATGAAAGTAGTATATCGTACTCCTCCGTCCAAAAAAAATCCAATCCTAGCTACGAACCTGAACATA
TATGTTCAGGTTCGTAGCTAGGATTGGATTTTTTTTGGACGGAGGAGTACGATATACTACTTTCATAATAAGTTTTATTTTTAGCCACTCTTATTTGTTC[A/G]
AATATAAATTTATTTCTAAATAATCATTACATCGAAATTTGTAAAAAGCAGGCTATAAATGTATCAAGAGTAAATAAAGTAGGAATAATCACATTGAGAC
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 | 70.80% | 29.20% | 0.04% | 0.00% | NA |
All Indica | 2759 | 98.60% | 1.30% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 18.30% | 81.70% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.60% | 2.20% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 44.80% | 55.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 14.10% | 85.90% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 25.00% | 75.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 61.10% | 38.90% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1018076166 | T -> C | LOC_Os10g33954.1 | downstream_gene_variant ; 4523.0bp to feature; MODIFIER | silent_mutation | Average:30.733; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
vg1018076166 | T -> C | LOC_Os10g33950-LOC_Os10g33954 | intergenic_region ; MODIFIER | silent_mutation | Average:30.733; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1018076166 | NA | 2.90E-21 | mr1217 | 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 |
vg1018076166 | NA | 1.31E-06 | mr1315 | 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 |
vg1018076166 | NA | 3.14E-12 | mr1386 | 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 |
vg1018076166 | NA | 4.81E-08 | mr1488 | 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 |
vg1018076166 | NA | 6.73E-20 | mr1845 | 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 |
vg1018076166 | NA | 1.51E-06 | mr1227_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 |
vg1018076166 | NA | 8.90E-18 | mr1336_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 |