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Detailed information for vg0803241893:

Variant ID: vg0803241893 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 3241893
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAAAATTAGAGATCAATCTTTCACAAGTTTAATAAAACTTTATCCTAACATTAAATATCTATGACCAAAGAGCATATATACTCTCTTTAAATGAACTAA[A/G]
CATCATCATACATAAATTAAGGTCCCGTTTGGATTATTTAGTCCCTGTATACTTTAGTCCTTGGACTAAAAACTGTAGTCCCCATTTGAATCCAGGGACT

Reverse complement sequence

AGTCCCTGGATTCAAATGGGGACTACAGTTTTTAGTCCAAGGACTAAAGTATACAGGGACTAAATAATCCAAACGGGACCTTAATTTATGTATGATGATG[T/C]
TTAGTTCATTTAAAGAGAGTATATATGCTCTTTGGTCATAGATATTTAATGTTAGGATAAAGTTTTATTAAACTTGTGAAAGATTGATCTCTAATTTTAT

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 93.40% 4.20% 0.11% 2.37% NA
All Indica  2759 99.90% 0.00% 0.00% 0.11% NA
All Japonica  1512 79.50% 13.00% 0.33% 7.21% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.00% 0.34% 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 99.90% 0.00% 0.00% 0.13% NA
Temperate Japonica  767 66.00% 20.50% 0.65% 12.91% NA
Tropical Japonica  504 98.80% 0.60% 0.00% 0.60% NA
Japonica Intermediate  241 82.20% 14.90% 0.00% 2.90% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0803241893 A -> G LOC_Os08g05950.1 upstream_gene_variant ; 1710.0bp to feature; MODIFIER silent_mutation Average:61.682; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N
vg0803241893 A -> G LOC_Os08g05960.1 upstream_gene_variant ; 895.0bp to feature; MODIFIER silent_mutation Average:61.682; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N
vg0803241893 A -> G LOC_Os08g05970.1 upstream_gene_variant ; 2728.0bp to feature; MODIFIER silent_mutation Average:61.682; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N
vg0803241893 A -> G LOC_Os08g05950-LOC_Os08g05960 intergenic_region ; MODIFIER silent_mutation Average:61.682; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N
vg0803241893 A -> DEL N N silent_mutation Average:61.682; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0803241893 3.47E-07 2.28E-10 mr1062 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
vg0803241893 6.83E-06 6.83E-06 mr1950 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
vg0803241893 4.52E-07 1.42E-06 mr1995 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
vg0803241893 NA 3.08E-09 mr1062_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