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Detailed information for vg1006264139:

Variant ID: vg1006264139 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 6264139
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGGTGTATTTCACGAAATGAAGTTAAAGTGAGTTATGTAAGATATATGCATGTGGGTATCACATGGCCCAATCAAAGGCTAAATGCCACTTCAGTGAAC[A/G]
GCAAGTGCATTTATATGGGCCATGTCGTGTTCGCCGACAGCATGGTGATGGATGAACAAAAGGTTCGCACAGCGAGGGAGTGACCGATGCCGTGCTCCTT

Reverse complement sequence

AAGGAGCACGGCATCGGTCACTCCCTCGCTGTGCGAACCTTTTGTTCATCCATCACCATGCTGTCGGCGAACACGACATGGCCCATATAAATGCACTTGC[T/C]
GTTCACTGAAGTGGCATTTAGCCTTTGATTGGGCCATGTGATACCCACATGCATATATCTTACATAACTCACTTTAACTTCATTTCGTGAAATACACCCG

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 96.10% 3.80% 0.06% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 88.50% 11.30% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 79.50% 20.20% 0.26% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 5.80% 0.41% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1006264139 A -> G LOC_Os10g11280.1 upstream_gene_variant ; 1205.0bp to feature; MODIFIER silent_mutation Average:50.172; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N
vg1006264139 A -> G LOC_Os10g11290.1 upstream_gene_variant ; 763.0bp to feature; MODIFIER silent_mutation Average:50.172; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N
vg1006264139 A -> G LOC_Os10g11280-LOC_Os10g11290 intergenic_region ; MODIFIER silent_mutation Average:50.172; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1006264139 2.65E-07 NA mr1062 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
vg1006264139 NA 6.97E-09 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
vg1006264139 7.39E-06 NA mr1210 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
vg1006264139 NA 1.44E-06 mr1210 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
vg1006264139 2.65E-06 NA mr1305 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
vg1006264139 NA 6.50E-07 mr1305 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
vg1006264139 2.12E-07 NA mr1586 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
vg1006264139 NA 1.82E-07 mr1586 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
vg1006264139 7.14E-06 NA mr1765 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
vg1006264139 NA 5.74E-07 mr1765 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
vg1006264139 NA 9.27E-06 mr1922 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
vg1006264139 NA 6.44E-07 mr1585_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