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Detailed information for vg0622463129:

Variant ID: vg0622463129 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22463129
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


AAATCGGCGTCTGAATCCGGCAGGGCTTCGCCCCTTCTTCTCTTCTCCTCCCCTCTCTTCTTTTTTTTTCACTGGAACTGAGGAGGGAGGAACGAGGGCT[G/A]
GGAGCTGGGCGGCAGGCCTTTTATAGGCAGCGAGGCCTGCCGCCCGGCCAGAGGGCGGCAAGGGGCCGCATGCAAAATGACCGGCCCCGACTGGCTTTTT

Reverse complement sequence

AAAAAGCCAGTCGGGGCCGGTCATTTTGCATGCGGCCCCTTGCCGCCCTCTGGCCGGGCGGCAGGCCTCGCTGCCTATAAAAGGCCTGCCGCCCAGCTCC[C/T]
AGCCCTCGTTCCTCCCTCCTCAGTTCCAGTGAAAAAAAAAGAAGAGAGGGGAGGAGAAGAGAAGAAGGGGCGAAGCCCTGCCGGATTCAGACGCCGATTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.70% 24.90% 8.29% 6.16% NA
All Indica  2759 37.80% 38.70% 13.41% 10.08% NA
All Japonica  1512 97.40% 2.00% 0.33% 0.33% NA
Aus  269 74.30% 19.70% 4.83% 1.12% NA
Indica I  595 16.00% 38.50% 26.39% 19.16% NA
Indica II  465 26.20% 44.10% 16.56% 13.12% NA
Indica III  913 60.20% 34.40% 3.50% 1.86% NA
Indica Intermediate  786 35.20% 40.60% 13.23% 10.94% NA
Temperate Japonica  767 98.60% 0.70% 0.39% 0.39% NA
Tropical Japonica  504 95.20% 4.60% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 0.80% 0.41% 0.83% NA
VI/Aromatic  96 93.80% 5.20% 0.00% 1.04% NA
Intermediate  90 67.80% 23.30% 4.44% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0622463129 G -> A LOC_Os06g37970.1 upstream_gene_variant ; 502.0bp to feature; MODIFIER silent_mutation Average:35.311; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0622463129 G -> A LOC_Os06g37990.1 upstream_gene_variant ; 3349.0bp to feature; MODIFIER silent_mutation Average:35.311; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0622463129 G -> A LOC_Os06g37980.1 downstream_gene_variant ; 1021.0bp to feature; MODIFIER silent_mutation Average:35.311; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0622463129 G -> A LOC_Os06g37970-LOC_Os06g37980 intergenic_region ; MODIFIER silent_mutation Average:35.311; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0622463129 G -> DEL N N silent_mutation Average:35.311; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622463129 NA 6.77E-07 mr1037 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
vg0622463129 NA 2.98E-08 mr1044 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
vg0622463129 NA 1.68E-06 mr1044 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
vg0622463129 NA 2.64E-06 mr1058 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
vg0622463129 8.99E-06 8.99E-06 mr1058 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
vg0622463129 NA 6.02E-08 mr1064 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
vg0622463129 NA 2.47E-06 mr1066 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
vg0622463129 NA 3.86E-07 mr1069 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
vg0622463129 NA 9.91E-06 mr1072 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
vg0622463129 NA 3.21E-07 mr1075 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
vg0622463129 NA 6.26E-06 mr1088 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
vg0622463129 NA 9.61E-07 mr1149 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
vg0622463129 NA 1.63E-06 mr1202 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
vg0622463129 NA 2.46E-06 mr1229 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
vg0622463129 NA 7.88E-06 mr1285 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
vg0622463129 5.03E-06 9.50E-06 mr1289 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
vg0622463129 NA 8.25E-06 mr1295 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
vg0622463129 NA 1.01E-12 mr1329 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
vg0622463129 NA 6.07E-10 mr1342 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
vg0622463129 NA 3.10E-06 mr1398 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
vg0622463129 NA 6.18E-08 mr1403 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
vg0622463129 NA 4.21E-06 mr1408 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
vg0622463129 3.52E-06 2.26E-06 mr1434 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
vg0622463129 NA 3.27E-06 mr1441 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
vg0622463129 NA 5.18E-06 mr1482 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
vg0622463129 NA 4.02E-06 mr1482 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
vg0622463129 NA 5.19E-06 mr1534 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
vg0622463129 NA 5.39E-06 mr1600 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
vg0622463129 NA 4.97E-06 mr1617 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
vg0622463129 7.33E-06 3.48E-06 mr1637 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
vg0622463129 NA 3.38E-06 mr1735 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
vg0622463129 NA 6.17E-06 mr1741 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
vg0622463129 7.52E-06 9.00E-11 mr1746 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
vg0622463129 3.87E-06 2.81E-08 mr1746 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
vg0622463129 NA 5.29E-06 mr1749 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
vg0622463129 NA 9.48E-08 mr1795 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
vg0622463129 NA 6.43E-07 mr1861 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
vg0622463129 NA 5.55E-06 mr1895 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
vg0622463129 NA 4.56E-06 mr1981 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
vg0622463129 NA 2.54E-07 mr1623_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