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Detailed information for vg0705453437:

Variant ID: vg0705453437 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 5453437
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TGTAGACAGTGTTGAGCTACTACTTAAGAGAGAGAAAGTGAGTGAGTGGTGGTCAGTAGTCATAGACTAAAGGCCCAACTTTTGCCTTAATGAACTGGTT[A/G]
CAAACATTAGTTTTAAAAGAAGAATGGGGATCGACTGGTGTGCATAAGTGCATGTTGGTATATTATTGTTTTCTCTCATAGATGTGAGTAAGTTTTGAAT

Reverse complement sequence

ATTCAAAACTTACTCACATCTATGAGAGAAAACAATAATATACCAACATGCACTTATGCACACCAGTCGATCCCCATTCTTCTTTTAAAACTAATGTTTG[T/C]
AACCAGTTCATTAAGGCAAAAGTTGGGCCTTTAGTCTATGACTACTGACCACCACTCACTCACTTTCTCTCTCTTAAGTAGTAGCTCAACACTGTCTACA

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% 6.60% 0.04% 0.00% NA
All Indica  2759 98.00% 2.00% 0.07% 0.00% NA
All Japonica  1512 96.60% 3.40% 0.00% 0.00% NA
Aus  269 27.50% 72.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.30% 0.25% 0.00% NA
Temperate Japonica  767 94.50% 5.50% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0705453437 A -> G LOC_Os07g10139.1 downstream_gene_variant ; 2862.0bp to feature; MODIFIER silent_mutation Average:61.388; most accessible tissue: Zhenshan97 flower, score: 75.194 N N N N
vg0705453437 A -> G LOC_Os07g10150.1 intron_variant ; MODIFIER silent_mutation Average:61.388; most accessible tissue: Zhenshan97 flower, score: 75.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0705453437 1.72E-06 1.72E-06 mr1197 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
vg0705453437 4.68E-08 1.40E-60 mr1549 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
vg0705453437 2.14E-13 1.42E-72 mr1550 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
vg0705453437 NA 3.05E-07 mr1621 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
vg0705453437 3.48E-16 3.83E-74 mr1757 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
vg0705453437 NA 1.71E-08 mr1757 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
vg0705453437 NA 1.34E-06 mr1762 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
vg0705453437 NA 8.88E-06 mr1928 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
vg0705453437 NA 5.31E-08 mr1931 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
vg0705453437 6.29E-29 5.82E-74 mr1549_2 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
vg0705453437 2.51E-13 1.06E-14 mr1549_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
vg0705453437 1.49E-24 4.46E-89 mr1550_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
vg0705453437 1.47E-09 2.68E-10 mr1550_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
vg0705453437 5.14E-23 1.01E-62 mr1757_2 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
vg0705453437 2.02E-10 2.80E-12 mr1757_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
vg0705453437 NA 3.66E-07 mr1762_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