Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0421387991:

Variant ID: vg0421387991 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21387991
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GATTTACGTGCAAAACTATTTTAAACCGATTTTTCTCTTAAATTAATTATCCAAATCATAATCCGATTACACCATTAAATTCGTTGCAATTAAATCTTCA[A/G]
AAAAAGACCACACATGGATATATTCCGACGAAAAAAATTAGCTTATTATTGATTTTTTTTAAATGTTGCACGATGTTCCACCAGGTATATCGGAATTGTC

Reverse complement sequence

GACAATTCCGATATACCTGGTGGAACATCGTGCAACATTTAAAAAAAATCAATAATAAGCTAATTTTTTTCGTCGGAATATATCCATGTGTGGTCTTTTT[T/C]
TGAAGATTTAATTGCAACGAATTTAATGGTGTAATCGGATTATGATTTGGATAATTAATTTAAGAGAAAAATCGGTTTAAAATAGTTTTGCACGTAAATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.60% 2.50% 0.38% 14.43% NA
All Indica  2759 78.80% 0.10% 0.22% 20.88% NA
All Japonica  1512 88.40% 5.30% 0.73% 5.56% NA
Aus  269 93.30% 1.90% 0.37% 4.46% NA
Indica I  595 86.10% 0.00% 0.17% 13.78% NA
Indica II  465 81.50% 0.00% 0.00% 18.49% NA
Indica III  913 72.20% 0.20% 0.44% 27.16% NA
Indica Intermediate  786 79.30% 0.30% 0.13% 20.36% NA
Temperate Japonica  767 97.50% 1.40% 0.39% 0.65% NA
Tropical Japonica  504 91.90% 4.40% 0.40% 3.37% NA
Japonica Intermediate  241 52.30% 19.50% 2.49% 25.73% NA
VI/Aromatic  96 70.80% 26.00% 0.00% 3.12% NA
Intermediate  90 85.60% 6.70% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0421387991 A -> DEL N N silent_mutation Average:51.358; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0421387991 A -> G LOC_Os04g35200.1 upstream_gene_variant ; 399.0bp to feature; MODIFIER silent_mutation Average:51.358; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0421387991 A -> G LOC_Os04g35190.1 downstream_gene_variant ; 2639.0bp to feature; MODIFIER silent_mutation Average:51.358; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0421387991 A -> G LOC_Os04g35200-LOC_Os04g35210 intergenic_region ; MODIFIER silent_mutation Average:51.358; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421387991 2.80E-07 2.80E-07 mr1098 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
vg0421387991 NA 1.72E-06 mr1101 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
vg0421387991 2.34E-07 2.85E-09 mr1113 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
vg0421387991 8.38E-08 2.44E-11 mr1114 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
vg0421387991 NA 4.66E-07 mr1116 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
vg0421387991 1.51E-07 3.08E-12 mr1117 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
vg0421387991 5.49E-06 1.87E-11 mr1118 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
vg0421387991 3.61E-07 4.00E-10 mr1119 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
vg0421387991 6.56E-09 2.94E-11 mr1120 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
vg0421387991 1.30E-09 1.30E-14 mr1123 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
vg0421387991 NA 1.45E-06 mr1150 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
vg0421387991 3.01E-06 3.01E-06 mr1197 Jap_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
vg0421387991 NA 1.18E-08 mr1240 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
vg0421387991 1.30E-08 1.23E-15 mr1242 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
vg0421387991 7.21E-10 9.65E-14 mr1247 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
vg0421387991 NA 6.70E-06 mr1441 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
vg0421387991 NA 1.54E-08 mr1495 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
vg0421387991 5.05E-06 1.52E-10 mr1496 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
vg0421387991 NA 9.56E-08 mr1693 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
vg0421387991 NA 6.29E-07 mr1736 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
vg0421387991 NA 1.68E-08 mr1917 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
vg0421387991 NA 4.72E-07 mr1936 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
vg0421387991 NA 6.74E-07 mr1961 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
vg0421387991 NA 8.89E-07 mr1098_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
vg0421387991 4.34E-08 1.68E-11 mr1113_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
vg0421387991 2.38E-10 7.12E-15 mr1114_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
vg0421387991 5.76E-11 6.46E-16 mr1117_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
vg0421387991 6.51E-10 3.35E-15 mr1118_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
vg0421387991 6.16E-10 7.85E-15 mr1119_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
vg0421387991 3.82E-09 5.63E-13 mr1120_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
vg0421387991 6.46E-11 6.83E-16 mr1123_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
vg0421387991 2.13E-06 2.06E-08 mr1150_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
vg0421387991 1.22E-11 1.33E-17 mr1240_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
vg0421387991 1.71E-09 2.77E-15 mr1242_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
vg0421387991 1.58E-09 8.65E-14 mr1247_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
vg0421387991 3.31E-09 9.60E-14 mr1495_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
vg0421387991 5.39E-11 3.68E-17 mr1496_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
vg0421387991 NA 4.58E-07 mr1691_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
vg0421387991 NA 3.75E-08 mr1861_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
vg0421387991 4.53E-09 8.93E-13 mr1936_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