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Detailed information for vg1122614316:

Variant ID: vg1122614316 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 22614316
Reference Allele: CAlternative Allele: T,CAA
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGCTGTTTGTTCATCCTAGAGAGGTCTCGACATGGTTCGAATAACATGGCTATTGATGTGGCATACTGCAGGCATCATCATAGAACAAATAATCATGTA[C/T,CAA]
ATTTTTTTTCTTGAGAACCCATATGCATGCCTCTTCACATTTAAAATAAAGACAAAATTGGTTTTATAGCATCAAACGTTTGTGATTTTTGTATGTTAGC

Reverse complement sequence

GCTAACATACAAAAATCACAAACGTTTGATGCTATAAAACCAATTTTGTCTTTATTTTAAATGTGAAGAGGCATGCATATGGGTTCTCAAGAAAAAAAAT[G/A,TTG]
TACATGATTATTTGTTCTATGATGATGCCTGCAGTATGCCACATCAATAGCCATGTTATTCGAACCATGTCGAGACCTCTCTAGGATGAACAAACAGCTT

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 69.10% 20.20% 6.73% 3.98% CAA: 0.04%
All Indica  2759 96.10% 3.50% 0.33% 0.07% NA
All Japonica  1512 13.60% 54.20% 20.11% 12.04% CAA: 0.13%
Aus  269 93.30% 5.90% 0.74% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 96.80% 2.80% 0.22% 0.22% NA
Indica III  913 94.50% 5.10% 0.33% 0.00% NA
Indica Intermediate  786 94.70% 4.70% 0.51% 0.13% NA
Temperate Japonica  767 10.20% 61.80% 20.34% 7.69% NA
Tropical Japonica  504 13.90% 40.90% 23.02% 21.83% CAA: 0.40%
Japonica Intermediate  241 23.70% 57.70% 13.28% 5.39% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 68.90% 23.30% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122614316 C -> T LOC_Os11g38130.1 upstream_gene_variant ; 1794.0bp to feature; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> T LOC_Os11g38140.1 downstream_gene_variant ; 561.0bp to feature; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> T LOC_Os11g38150.1 downstream_gene_variant ; 4503.0bp to feature; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> T LOC_Os11g38130-LOC_Os11g38140 intergenic_region ; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> CAA LOC_Os11g38130.1 upstream_gene_variant ; 1795.0bp to feature; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> CAA LOC_Os11g38140.1 downstream_gene_variant ; 560.0bp to feature; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> CAA LOC_Os11g38150.1 downstream_gene_variant ; 4502.0bp to feature; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> CAA LOC_Os11g38130-LOC_Os11g38140 intergenic_region ; MODIFIER silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N
vg1122614316 C -> DEL N N silent_mutation Average:54.761; most accessible tissue: Callus, score: 98.346 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122614316 NA 2.14E-08 mr1071 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
vg1122614316 NA 4.35E-09 mr1100 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
vg1122614316 NA 3.30E-09 mr1140 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
vg1122614316 NA 1.72E-07 mr1203 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
vg1122614316 NA 4.30E-08 mr1395 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
vg1122614316 6.42E-08 1.34E-12 mr1613 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
vg1122614316 NA 2.70E-08 mr1618 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
vg1122614316 NA 1.83E-07 mr1619 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
vg1122614316 NA 5.27E-20 mr1715 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
vg1122614316 9.04E-07 9.04E-07 mr1795 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
vg1122614316 NA 1.17E-19 mr1913 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
vg1122614316 2.85E-06 4.71E-13 mr1913 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
vg1122614316 NA 7.29E-09 mr1986 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
vg1122614316 NA 9.18E-08 mr1071_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
vg1122614316 NA 1.32E-06 mr1080_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
vg1122614316 NA 1.11E-08 mr1100_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
vg1122614316 NA 2.01E-08 mr1203_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
vg1122614316 NA 1.80E-08 mr1613_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
vg1122614316 NA 1.41E-07 mr1913_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
vg1122614316 NA 4.71E-06 mr1962_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