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Detailed information for vg1124840128:

Variant ID: vg1124840128 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24840128
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


CGTGCCTTGCACGTGCACACTCACTAGTATTTTAAAATGGATGAGTAGATTTATAGATTTACTCCCTCCATTTCAAAATATAAGACCCGGCCACTATTAA[T/C]
GCAAAGACAAAAAAAAATATTATCACCTTTTTGTTAGGATCACCCAAATAAATAAAATGCATGCACCCAATGGGAATAGAGTTATTGAGAATGGAGGATT

Reverse complement sequence

AATCCTCCATTCTCAATAACTCTATTCCCATTGGGTGCATGCATTTTATTTATTTGGGTGATCCTAACAAAAAGGTGATAATATTTTTTTTTGTCTTTGC[A/G]
TTAATAGTGGCCGGGTCTTATATTTTGAAATGGAGGGAGTAAATCTATAAATCTACTCATCCATTTTAAAATACTAGTGAGTGTGCACGTGCAAGGCACG

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 88.50% 10.80% 0.66% 0.00% NA
All Indica  2759 92.30% 7.60% 0.11% 0.00% NA
All Japonica  1512 79.10% 19.10% 1.79% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 95.00% 4.90% 0.17% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 90.80% 9.20% 0.00% 0.00% NA
Indica Intermediate  786 88.50% 11.20% 0.25% 0.00% NA
Temperate Japonica  767 64.10% 32.30% 3.52% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 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
vg1124840128 T -> C LOC_Os11g41380.1 downstream_gene_variant ; 3336.0bp to feature; MODIFIER silent_mutation Average:27.667; most accessible tissue: Zhenshan97 young leaf, score: 55.899 N N N N
vg1124840128 T -> C LOC_Os11g41400.1 downstream_gene_variant ; 3910.0bp to feature; MODIFIER silent_mutation Average:27.667; most accessible tissue: Zhenshan97 young leaf, score: 55.899 N N N N
vg1124840128 T -> C LOC_Os11g41390.1 intron_variant ; MODIFIER silent_mutation Average:27.667; most accessible tissue: Zhenshan97 young leaf, score: 55.899 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124840128 8.29E-06 NA mr1238 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
vg1124840128 1.97E-07 3.16E-06 mr1309 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
vg1124840128 2.73E-06 NA mr1841 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
vg1124840128 6.44E-06 NA mr1841 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
vg1124840128 3.20E-06 NA mr1900 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
vg1124840128 7.76E-06 NA mr1900 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
vg1124840128 5.01E-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
vg1124840128 3.40E-07 NA mr1238_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
vg1124840128 NA 3.97E-06 mr1533_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
vg1124840128 1.69E-08 NA mr1609_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
vg1124840128 3.31E-08 3.31E-08 mr1609_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
vg1124840128 6.06E-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
vg1124840128 9.98E-08 NA mr1841_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
vg1124840128 6.55E-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
vg1124840128 1.58E-07 NA mr1900_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