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Detailed information for vg0725374896:

Variant ID: vg0725374896 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25374896
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: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGTCTCCAAGGCTTCAGTGCAATGATTCAAGTAACCAATCTGCAAGATTCATTCTCCTTGTTTTCCCCCTGTATGTGCTGTGGCTGATAAAGTTTTCT[A/G]
TCTTGGTTAACTGCAGGACACTCCTGTTTCTAATATGCATGAGAATTCATTTCGCAGAAGCTCATGATGCAGGTATCATACATGATTATGAATTATTAAT

Reverse complement sequence

ATTAATAATTCATAATCATGTATGATACCTGCATCATGAGCTTCTGCGAAATGAATTCTCATGCATATTAGAAACAGGAGTGTCCTGCAGTTAACCAAGA[T/C]
AGAAAACTTTATCAGCCACAGCACATACAGGGGGAAAACAAGGAGAATGAATCTTGCAGATTGGTTACTTGAATCATTGCACTGAAGCCTTGGAGACCAT

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 92.00% 8.00% 0.02% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 76.30% 23.70% 0.00% 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 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 96.20% 3.80% 0.00% 0.00% NA
Tropical Japonica  504 42.50% 57.50% 0.00% 0.00% NA
Japonica Intermediate  241 83.40% 16.60% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 1.11% 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
vg0725374896 A -> G LOC_Os07g42395.1 upstream_gene_variant ; 3089.0bp to feature; MODIFIER silent_mutation Average:49.591; most accessible tissue: Zhenshan97 flower, score: 65.164 N N N N
vg0725374896 A -> G LOC_Os07g42395.2 upstream_gene_variant ; 3040.0bp to feature; MODIFIER silent_mutation Average:49.591; most accessible tissue: Zhenshan97 flower, score: 65.164 N N N N
vg0725374896 A -> G LOC_Os07g42400.1 intron_variant ; MODIFIER silent_mutation Average:49.591; most accessible tissue: Zhenshan97 flower, score: 65.164 N N N N
vg0725374896 A -> G LOC_Os07g42400.2 intron_variant ; MODIFIER silent_mutation Average:49.591; most accessible tissue: Zhenshan97 flower, score: 65.164 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725374896 NA 8.12E-11 mr1055 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
vg0725374896 NA 2.05E-10 mr1132 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
vg0725374896 NA 1.40E-06 mr1248 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
vg0725374896 NA 2.87E-18 mr1301 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
vg0725374896 NA 3.85E-09 mr1563 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
vg0725374896 NA 7.09E-08 mr1825 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
vg0725374896 NA 1.37E-06 mr1993 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
vg0725374896 NA 1.38E-13 mr1178_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
vg0725374896 NA 5.96E-06 mr1498_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
vg0725374896 NA 1.14E-11 mr1769_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
vg0725374896 NA 9.95E-14 mr1769_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
vg0725374896 NA 2.95E-11 mr1993_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