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Detailed information for vg0621576738:

Variant ID: vg0621576738 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21576738
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.78, G: 0.21, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTATTTATACCCATAGGTGTCCCCTTGTCCAAGTAGAACTAGGGAAACCAATATGGATACAATCCGAGTAGTCCTTGTCGTTTCCATATAGAACTTTG[A/G]
TTGTCTTTTCTCATCGGAACTCCTCCTATATCCGAAGGTTGTTTCCGTATAGGACATGGTATGTGGTGGGTCCTGCCGAGATTTAGTCAACTACTATTAG

Reverse complement sequence

CTAATAGTAGTTGACTAAATCTCGGCAGGACCCACCACATACCATGTCCTATACGGAAACAACCTTCGGATATAGGAGGAGTTCCGATGAGAAAAGACAA[T/C]
CAAAGTTCTATATGGAAACGACAAGGACTACTCGGATTGTATCCATATTGGTTTCCCTAGTTCTACTTGGACAAGGGGACACCTATGGGTATAAATACAA

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 67.70% 24.00% 5.14% 3.17% NA
All Indica  2759 66.90% 26.40% 1.38% 5.29% NA
All Japonica  1512 85.30% 5.80% 8.80% 0.20% NA
Aus  269 0.00% 98.10% 1.86% 0.00% NA
Indica I  595 94.50% 4.70% 0.67% 0.17% NA
Indica II  465 77.40% 21.50% 1.08% 0.00% NA
Indica III  913 44.90% 44.00% 1.31% 9.75% NA
Indica Intermediate  786 65.40% 25.30% 2.16% 7.12% NA
Temperate Japonica  767 83.70% 0.70% 15.25% 0.39% NA
Tropical Japonica  504 84.50% 14.50% 0.99% 0.00% NA
Japonica Intermediate  241 91.70% 3.70% 4.56% 0.00% NA
VI/Aromatic  96 4.20% 34.40% 61.46% 0.00% NA
Intermediate  90 68.90% 21.10% 8.89% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0621576738 A -> G LOC_Os06g36690.1 upstream_gene_variant ; 190.0bp to feature; MODIFIER silent_mutation Average:52.585; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N
vg0621576738 A -> G LOC_Os06g36690-LOC_Os06g36700 intergenic_region ; MODIFIER silent_mutation Average:52.585; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N
vg0621576738 A -> DEL N N silent_mutation Average:52.585; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621576738 NA 1.23E-06 mr1215 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
vg0621576738 NA 9.14E-06 mr1422 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
vg0621576738 NA 8.89E-09 mr1583 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
vg0621576738 NA 7.52E-08 mr1126_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
vg0621576738 NA 1.96E-08 mr1218_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
vg0621576738 NA 1.00E-08 mr1221_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
vg0621576738 NA 1.42E-06 mr1522_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
vg0621576738 NA 7.07E-17 mr1583_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
vg0621576738 NA 1.38E-08 mr1583_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
vg0621576738 4.42E-06 NA mr1631_2 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
vg0621576738 NA 8.32E-09 mr1850_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