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Detailed information for vg0625197129:

Variant ID: vg0625197129 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25197129
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAATTGAATGATGTAATCGGATGGATAAATAATTTAAGAGAAACAATAGTTTAAAGTAGTTTTTGCATGCTGATGTCAGCATGACGTGGACGCTCAATGT[G/A]
TAGTTGCCTCCGTATTTGTTACAATTAAATCTTTACAACAAGATCTCACTCGATTATATTCTGATTATTTTTTAAAACTTATTTTGTATTGTTGCGCATA

Reverse complement sequence

TATGCGCAACAATACAAAATAAGTTTTAAAAAATAATCAGAATATAATCGAGTGAGATCTTGTTGTAAAGATTTAATTGTAACAAATACGGAGGCAACTA[C/T]
ACATTGAGCGTCCACGTCATGCTGACATCAGCATGCAAAAACTACTTTAAACTATTGTTTCTCTTAAATTATTTATCCATCCGATTACATCATTCAATTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.60% 11.40% 0.00% 0.00% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 69.00% 31.00% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 87.10% 12.90% 0.00% 0.00% NA
Tropical Japonica  504 53.40% 46.60% 0.00% 0.00% NA
Japonica Intermediate  241 44.40% 55.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0625197129 G -> A LOC_Os06g41980.1 upstream_gene_variant ; 1113.0bp to feature; MODIFIER silent_mutation Average:26.439; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N
vg0625197129 G -> A LOC_Os06g41990.1 downstream_gene_variant ; 3147.0bp to feature; MODIFIER silent_mutation Average:26.439; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N
vg0625197129 G -> A LOC_Os06g41990.2 downstream_gene_variant ; 3147.0bp to feature; MODIFIER silent_mutation Average:26.439; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N
vg0625197129 G -> A LOC_Os06g41970-LOC_Os06g41980 intergenic_region ; MODIFIER silent_mutation Average:26.439; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625197129 1.52E-06 NA mr1086 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
vg0625197129 6.33E-06 NA mr1104 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
vg0625197129 9.11E-08 NA mr1107 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
vg0625197129 6.66E-06 NA mr1213 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
vg0625197129 5.66E-08 NA mr1226 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
vg0625197129 NA 4.01E-08 mr1408 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
vg0625197129 1.54E-09 NA mr1411 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
vg0625197129 8.76E-07 NA mr1560 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
vg0625197129 2.56E-06 1.78E-11 mr1949 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
vg0625197129 3.07E-06 NA mr1104_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
vg0625197129 NA 5.17E-07 mr1183_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
vg0625197129 7.86E-06 NA mr1226_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
vg0625197129 NA 9.78E-08 mr1861_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