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Detailed information for vg0311535858:

Variant ID: vg0311535858 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 11535858
Reference Allele: AAlternative Allele: C,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAAAAAATTATGCCACAATGGACCAAAATACCCTTGTACACATCAATATTCTCTTATCCTCTCCCTCTCATCTCTCTCACCGGAGCTTGTCTCCCTCT[A/C,T]
ATCTTTCTCGCCAGAAATGGGAGGGATAGCGGCGGCGGCTCGACGAGGAGGAGGAGCGGCGACGGCTCGACAAGGCGGAGGACGGCGGCGGCATGGGAGG

Reverse complement sequence

CCTCCCATGCCGCCGCCGTCCTCCGCCTTGTCGAGCCGTCGCCGCTCCTCCTCCTCGTCGAGCCGCCGCCGCTATCCCTCCCATTTCTGGCGAGAAAGAT[T/G,A]
AGAGGGAGACAAGCTCCGGTGAGAGAGATGAGAGGGAGAGGATAAGAGAATATTGATGTGTACAAGGGTATTTTGGTCCATTGTGGCATAATTTTTTTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.10% 19.70% 0.02% 0.00% T: 0.19%
All Indica  2759 99.80% 0.10% 0.04% 0.00% T: 0.04%
All Japonica  1512 39.70% 60.30% 0.00% 0.00% NA
Aus  269 97.00% 0.00% 0.00% 0.00% T: 2.97%
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.13% 0.00% T: 0.13%
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 40.20% 59.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0311535858 A -> C LOC_Os03g20380.1 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380.4 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380.5 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380.8 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380.7 upstream_gene_variant ; 4742.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380.2 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380.3 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380.6 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> C LOC_Os03g20380-LOC_Os03g20390 intergenic_region ; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.1 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.4 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.5 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.8 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.7 upstream_gene_variant ; 4742.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.2 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.3 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380.6 upstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N
vg0311535858 A -> T LOC_Os03g20380-LOC_Os03g20390 intergenic_region ; MODIFIER silent_mutation Average:49.477; most accessible tissue: Minghui63 flag leaf, score: 70.648 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0311535858 NA 1.37E-25 mr1115 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
vg0311535858 NA 1.02E-16 mr1115 Jap_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
vg0311535858 NA 2.41E-21 mr1163 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
vg0311535858 NA 1.89E-07 mr1229 Jap_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
vg0311535858 NA 4.73E-40 mr1235 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
vg0311535858 8.32E-06 5.28E-61 mr1241 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
vg0311535858 NA 7.65E-15 mr1241 Jap_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
vg0311535858 NA 4.08E-10 mr1277 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
vg0311535858 NA 5.07E-06 mr1277 Jap_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
vg0311535858 NA 2.06E-86 mr1334 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
vg0311535858 NA 8.79E-08 mr1403 Jap_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
vg0311535858 NA 5.33E-32 mr1448 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
vg0311535858 NA 3.34E-37 mr1486 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
vg0311535858 NA 3.37E-35 mr1533 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
vg0311535858 NA 7.47E-25 mr1611 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
vg0311535858 NA 9.11E-13 mr1611 Jap_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
vg0311535858 NA 9.37E-07 mr1671 Jap_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
vg0311535858 NA 4.05E-07 mr1763 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
vg0311535858 NA 1.21E-72 mr1778 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
vg0311535858 NA 1.73E-32 mr1789 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
vg0311535858 NA 3.93E-15 mr1844 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
vg0311535858 NA 3.72E-07 mr1844 Jap_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
vg0311535858 NA 8.79E-13 mr1879 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
vg0311535858 NA 1.70E-09 mr1880 Jap_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
vg0311535858 NA 1.38E-24 mr1920 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
vg0311535858 NA 1.29E-07 mr1993 Jap_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
vg0311535858 NA 1.30E-24 mr1115_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
vg0311535858 NA 2.00E-67 mr1241_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
vg0311535858 NA 2.42E-12 mr1241_2 Jap_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
vg0311535858 NA 2.92E-15 mr1277_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
vg0311535858 NA 2.71E-23 mr1304_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
vg0311535858 NA 2.48E-08 mr1304_2 Jap_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
vg0311535858 NA 3.38E-23 mr1308_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
vg0311535858 NA 1.62E-07 mr1308_2 Jap_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
vg0311535858 NA 1.09E-95 mr1334_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
vg0311535858 NA 3.35E-22 mr1361_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
vg0311535858 NA 2.07E-35 mr1368_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
vg0311535858 NA 4.21E-11 mr1368_2 Jap_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
vg0311535858 NA 1.31E-07 mr1401_2 Jap_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
vg0311535858 NA 1.52E-08 mr1454_2 Jap_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
vg0311535858 NA 2.69E-44 mr1486_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
vg0311535858 NA 2.10E-29 mr1584_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
vg0311535858 NA 1.29E-09 mr1584_2 Jap_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
vg0311535858 NA 1.27E-16 mr1730_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
vg0311535858 NA 1.69E-16 mr1746_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
vg0311535858 NA 3.02E-73 mr1778_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
vg0311535858 NA 4.20E-29 mr1789_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
vg0311535858 NA 5.41E-07 mr1798_2 Jap_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
vg0311535858 NA 1.91E-12 mr1853_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
vg0311535858 NA 2.12E-15 mr1866_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
vg0311535858 NA 4.00E-18 mr1980_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