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Detailed information for vg1125063819:

Variant ID: vg1125063819 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25063819
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGACAACTTACAGAGTGTCTTAAGTCAAATGTCTTATAACAGTGGTTTTGTTGTAGTGCGCTCCACTACGGCAGAAGCTGGCCTTTATTAAGTGCAAAT[G/A]
AAATTGGATCACAACTCAACAGATACAACTCTACTTCCACTTCGATGATCTGCTGCTCATGTAGTTCTATATATTGTCTGCACTTTGTAGCTTGAGAGCC

Reverse complement sequence

GGCTCTCAAGCTACAAAGTGCAGACAATATATAGAACTACATGAGCAGCAGATCATCGAAGTGGAAGTAGAGTTGTATCTGTTGAGTTGTGATCCAATTT[C/T]
ATTTGCACTTAATAAAGGCCAGCTTCTGCCGTAGTGGAGCGCACTACAACAAAACCACTGTTATAAGACATTTGACTTAAGACACTCTGTAAGTTGTCTC

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 49.50% 44.10% 2.39% 4.02% NA
All Indica  2759 33.70% 65.00% 1.38% 0.00% NA
All Japonica  1512 73.10% 13.00% 1.59% 12.37% NA
Aus  269 71.00% 19.30% 9.29% 0.37% NA
Indica I  595 8.20% 91.30% 0.50% 0.00% NA
Indica II  465 32.30% 67.50% 0.22% 0.00% NA
Indica III  913 45.50% 52.00% 2.52% 0.00% NA
Indica Intermediate  786 40.10% 58.50% 1.40% 0.00% NA
Temperate Japonica  767 73.80% 3.50% 2.22% 20.47% NA
Tropical Japonica  504 71.40% 26.80% 0.60% 1.19% NA
Japonica Intermediate  241 74.30% 14.10% 1.66% 9.96% NA
VI/Aromatic  96 74.00% 3.10% 21.88% 1.04% NA
Intermediate  90 48.90% 44.40% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125063819 G -> A LOC_Os11g41740.1 missense_variant ; p.Ser152Leu; MODERATE nonsynonymous_codon ; S152L Average:34.226; most accessible tissue: Zhenshan97 root, score: 64.819 unknown unknown DELETERIOUS 0.00
vg1125063819 G -> DEL LOC_Os11g41740.1 N frameshift_variant Average:34.226; most accessible tissue: Zhenshan97 root, score: 64.819 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125063819 1.88E-09 NA mr1238 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
vg1125063819 2.37E-07 2.28E-08 mr1238 Ind_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
vg1125063819 1.89E-09 3.00E-27 mr1309 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
vg1125063819 1.22E-08 4.23E-10 mr1309 Ind_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
vg1125063819 1.63E-06 2.48E-16 mr1609 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
vg1125063819 5.89E-09 1.38E-28 mr1841 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
vg1125063819 NA 4.92E-07 mr1841 Ind_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
vg1125063819 NA 5.45E-10 mr1945 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
vg1125063819 7.05E-06 NA mr1238_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
vg1125063819 9.55E-07 9.61E-25 mr1609_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
vg1125063819 2.55E-07 NA mr1841_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
vg1125063819 4.64E-07 NA mr1900_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