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Detailed information for vg0107138425:

Variant ID: vg0107138425 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7138425
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTCATTGTTGTTAGATGATAAAACATGATTAATACTTTATGCATGTCTTATCTTTTTAATTTTTTTTAAATAAGACGGAGGGTCAAACGTTGGACACG[A/G]
AAACCCAGGGTTTGTCTTTTTTTTAGGACAGAGGGATTACGTAGCAAGACTATTTACGACCTTTTTATCCATACATCCACGATAGGAACTTGCAACTGGA

Reverse complement sequence

TCCAGTTGCAAGTTCCTATCGTGGATGTATGGATAAAAAGGTCGTAAATAGTCTTGCTACGTAATCCCTCTGTCCTAAAAAAAAGACAAACCCTGGGTTT[T/C]
CGTGTCCAACGTTTGACCCTCCGTCTTATTTAAAAAAAATTAAAAAGATAAGACATGCATAAAGTATTAATCATGTTTTATCATCTAACAACAATGAAAA

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 71.40% 28.30% 0.15% 0.17% NA
All Indica  2759 97.40% 2.10% 0.22% 0.29% NA
All Japonica  1512 18.50% 81.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.00% 0.17% NA
Indica II  465 99.40% 0.40% 0.00% 0.22% NA
Indica III  913 97.80% 1.20% 0.44% 0.55% NA
Indica Intermediate  786 94.40% 5.20% 0.25% 0.13% NA
Temperate Japonica  767 2.10% 97.90% 0.00% 0.00% NA
Tropical Japonica  504 48.00% 52.00% 0.00% 0.00% NA
Japonica Intermediate  241 8.70% 91.30% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 70.00% 28.90% 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
vg0107138425 A -> G LOC_Os01g12880.1 downstream_gene_variant ; 1095.0bp to feature; MODIFIER silent_mutation Average:77.038; most accessible tissue: Zhenshan97 flower, score: 88.302 N N N N
vg0107138425 A -> G LOC_Os01g12880-LOC_Os01g12890 intergenic_region ; MODIFIER silent_mutation Average:77.038; most accessible tissue: Zhenshan97 flower, score: 88.302 N N N N
vg0107138425 A -> DEL N N silent_mutation Average:77.038; most accessible tissue: Zhenshan97 flower, score: 88.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107138425 NA 4.23E-09 mr1005 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
vg0107138425 NA 4.29E-58 mr1019 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
vg0107138425 NA 7.47E-07 mr1364 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
vg0107138425 NA 2.69E-07 mr1443 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
vg0107138425 NA 3.69E-09 mr1575 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
vg0107138425 NA 1.69E-14 mr1653 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
vg0107138425 NA 9.55E-84 mr1672 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
vg0107138425 NA 4.84E-40 mr1243_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
vg0107138425 5.60E-08 NA mr1498_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
vg0107138425 4.34E-09 3.76E-11 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
vg0107138425 NA 6.64E-25 mr1653_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
vg0107138425 NA 7.63E-69 mr1733_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
vg0107138425 NA 1.07E-09 mr1947_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