Variant ID: vg0203428380 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 3428380 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGTGTTCAACCCTAACTTCCAACTTTCCATCACATCACATCACATCCAAAACTTTCCTACACACATAAACTTCCAATTTTTTTTCCAAACTTCCAACTTT[C/T]
CCCAAACTTCCAACTTTTTTCAGGAACTAAACACAGCCTTAGTCTTATTAATCTAAATATCAAGGCCGACAAAAAGGAAAAGAATTATTTGATTCCAAGC
GCTTGGAATCAAATAATTCTTTTCCTTTTTGTCGGCCTTGATATTTAGATTAATAAGACTAAGGCTGTGTTTAGTTCCTGAAAAAAGTTGGAAGTTTGGG[G/A]
AAAGTTGGAAGTTTGGAAAAAAAATTGGAAGTTTATGTGTGTAGGAAAGTTTTGGATGTGATGTGATGTGATGGAAAGTTGGAAGTTAGGGTTGAACACA
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 | 37.80% | 2.70% | 23.36% | 36.16% | NA |
All Indica | 2759 | 20.70% | 4.50% | 38.42% | 36.39% | NA |
All Japonica | 1512 | 61.80% | 0.10% | 1.52% | 36.57% | NA |
Aus | 269 | 85.10% | 0.00% | 1.49% | 13.38% | NA |
Indica I | 595 | 12.60% | 4.20% | 44.03% | 39.16% | NA |
Indica II | 465 | 24.50% | 0.40% | 35.48% | 39.57% | NA |
Indica III | 913 | 23.20% | 8.80% | 36.80% | 31.22% | NA |
Indica Intermediate | 786 | 21.60% | 2.20% | 37.79% | 38.42% | NA |
Temperate Japonica | 767 | 70.40% | 0.00% | 0.91% | 28.68% | NA |
Tropical Japonica | 504 | 55.80% | 0.20% | 2.18% | 41.87% | NA |
Japonica Intermediate | 241 | 47.30% | 0.00% | 2.07% | 50.62% | NA |
VI/Aromatic | 96 | 6.20% | 0.00% | 1.04% | 92.71% | NA |
Intermediate | 90 | 51.10% | 1.10% | 17.78% | 30.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0203428380 | C -> T | LOC_Os02g06779.1 | upstream_gene_variant ; 4934.0bp to feature; MODIFIER | silent_mutation | Average:13.355; most accessible tissue: Callus, score: 58.161 | N | N | N | N |
vg0203428380 | C -> T | LOC_Os02g06790.1 | downstream_gene_variant ; 167.0bp to feature; MODIFIER | silent_mutation | Average:13.355; most accessible tissue: Callus, score: 58.161 | N | N | N | N |
vg0203428380 | C -> T | LOC_Os02g06779-LOC_Os02g06790 | intergenic_region ; MODIFIER | silent_mutation | Average:13.355; most accessible tissue: Callus, score: 58.161 | N | N | N | N |
vg0203428380 | C -> DEL | N | N | silent_mutation | Average:13.355; most accessible tissue: Callus, score: 58.161 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0203428380 | NA | 5.34E-10 | mr1201 | 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 |
vg0203428380 | NA | 7.27E-11 | mr1201 | 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 |
vg0203428380 | NA | 4.84E-07 | mr1219 | 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 |
vg0203428380 | NA | 4.14E-09 | mr1219 | 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 |
vg0203428380 | NA | 3.17E-10 | mr1274 | 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 |
vg0203428380 | NA | 1.98E-09 | mr1274 | 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 |
vg0203428380 | 7.49E-06 | 3.95E-14 | mr1201_2 | 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 |
vg0203428380 | 3.30E-06 | 3.38E-15 | mr1201_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 |
vg0203428380 | NA | 4.57E-09 | mr1219_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 |
vg0203428380 | NA | 2.17E-12 | mr1219_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 |
vg0203428380 | NA | 5.61E-14 | mr1274_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 |
vg0203428380 | NA | 5.83E-14 | mr1274_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 |