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Detailed information for vg1123553400:

Variant ID: vg1123553400 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23553400
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, T: 0.25, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGGGTTGGTGACCACTCCAAGATCTCAAAATATAACCAAAGCTGGTGCATGGTTATCAAATCCAAACTCTGAAAATACTTTGGGGGTCACACCAAGAC[C/T]
CAAGCGAGGGCCAAAAAAAAAGAAACTACAGAAGAAAGGGAAAAATAAAGGTGATTTCCACGGCTCCCATGATAAATGTCGCAAGTTCAGTAGCAGTATT

Reverse complement sequence

AATACTGCTACTGAACTTGCGACATTTATCATGGGAGCCGTGGAAATCACCTTTATTTTTCCCTTTCTTCTGTAGTTTCTTTTTTTTTGGCCCTCGCTTG[G/A]
GTCTTGGTGTGACCCCCAAAGTATTTTCAGAGTTTGGATTTGATAACCATGCACCAGCTTTGGTTATATTTTGAGATCTTGGAGTGGTCACCAACCCAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 29.10% 18.00% 3.34% 49.62% NA
All Indica  2759 20.60% 9.60% 1.78% 68.00% NA
All Japonica  1512 45.60% 32.20% 6.55% 15.61% NA
Aus  269 27.10% 4.50% 0.00% 68.40% NA
Indica I  595 29.60% 6.70% 3.36% 60.34% NA
Indica II  465 6.90% 3.00% 0.65% 89.46% NA
Indica III  913 19.60% 16.60% 0.88% 62.87% NA
Indica Intermediate  786 23.20% 7.50% 2.29% 67.05% NA
Temperate Japonica  767 70.50% 16.20% 6.00% 7.30% NA
Tropical Japonica  504 18.70% 53.40% 7.54% 20.44% NA
Japonica Intermediate  241 22.80% 39.00% 6.22% 31.95% NA
VI/Aromatic  96 15.60% 66.70% 6.25% 11.46% NA
Intermediate  90 30.00% 23.30% 4.44% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1123553400 C -> T LOC_Os11g39540.1 downstream_gene_variant ; 160.0bp to feature; MODIFIER silent_mutation Average:39.344; most accessible tissue: Minghui63 flower, score: 74.23 N N N N
vg1123553400 C -> T LOC_Os11g39530-LOC_Os11g39540 intergenic_region ; MODIFIER silent_mutation Average:39.344; most accessible tissue: Minghui63 flower, score: 74.23 N N N N
vg1123553400 C -> DEL N N silent_mutation Average:39.344; most accessible tissue: Minghui63 flower, score: 74.23 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123553400 NA 3.42E-11 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1123553400 NA 3.21E-06 mr1164 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
vg1123553400 NA 8.25E-06 mr1192 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
vg1123553400 NA 1.45E-06 mr1205 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
vg1123553400 NA 2.28E-07 mr1229 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
vg1123553400 NA 1.09E-07 mr1280 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
vg1123553400 NA 1.70E-06 mr1318 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
vg1123553400 NA 5.73E-07 mr1330 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
vg1123553400 NA 7.00E-06 mr1332 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
vg1123553400 NA 2.53E-06 mr1521 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
vg1123553400 NA 1.17E-08 mr1531 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
vg1123553400 NA 9.92E-06 mr1596 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
vg1123553400 NA 8.07E-08 mr1617 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
vg1123553400 NA 3.15E-07 mr1627 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
vg1123553400 NA 2.56E-07 mr1729 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
vg1123553400 NA 3.49E-06 mr1741 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
vg1123553400 NA 6.89E-07 mr1788 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
vg1123553400 NA 9.96E-06 mr1063_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
vg1123553400 NA 2.01E-07 mr1229_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
vg1123553400 NA 6.20E-09 mr1521_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
vg1123553400 NA 3.19E-08 mr1557_2 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
vg1123553400 NA 2.48E-06 mr1693_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
vg1123553400 NA 2.84E-06 mr1703_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
vg1123553400 NA 1.58E-07 mr1880_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