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Detailed information for vg0129059051:

Variant ID: vg0129059051 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29059051
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTATTTTGTTATGAGTTGTTTTATCACTTATAGTATTTTAAGTGTGATTTATATCTTATATATTTGTATAAAATTTTTGAATAAGACGAATGGTTAAA[T/C]
ATGTGAGAAAAAGTTAATGGCGTCATCTATTAAAAAACTAAAGGATTATATGCTAATGACTTAGGAGTACATCGCTTTTCATGCAGCTAACTAGCTAATC

Reverse complement sequence

GATTAGCTAGTTAGCTGCATGAAAAGCGATGTACTCCTAAGTCATTAGCATATAATCCTTTAGTTTTTTAATAGATGACGCCATTAACTTTTTCTCACAT[A/G]
TTTAACCATTCGTCTTATTCAAAAATTTTATACAAATATATAAGATATAAATCACACTTAAAATACTATAAGTGATAAAACAACTCATAACAAAATAAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.40% 14.50% 0.15% 0.00% NA
All Indica  2759 97.90% 2.00% 0.04% 0.00% NA
All Japonica  1512 61.60% 38.40% 0.07% 0.00% NA
Aus  269 91.80% 7.10% 1.12% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.50% 0.13% 0.00% NA
Temperate Japonica  767 88.40% 11.60% 0.00% 0.00% NA
Tropical Japonica  504 32.10% 67.70% 0.20% 0.00% NA
Japonica Intermediate  241 37.80% 62.20% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 80.00% 17.80% 2.22% 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
vg0129059051 T -> C LOC_Os01g50610-LOC_Os01g50616 intergenic_region ; MODIFIER silent_mutation Average:41.555; most accessible tissue: Callus, score: 70.622 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129059051 7.81E-06 7.81E-06 mr1160 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
vg0129059051 1.62E-06 NA mr1679 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
vg0129059051 NA 9.97E-09 mr1693 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
vg0129059051 NA 9.01E-20 mr1042_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
vg0129059051 NA 4.73E-07 mr1369_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
vg0129059051 NA 7.08E-08 mr1453_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
vg0129059051 NA 1.59E-06 mr1662_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
vg0129059051 NA 3.42E-10 mr1680_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
vg0129059051 NA 2.59E-07 mr1691_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
vg0129059051 NA 4.31E-22 mr1871_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
vg0129059051 NA 2.17E-08 mr1871_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