\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1209095184:

Variant ID: vg1209095184 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 9095184
Reference Allele: CAlternative Allele: CTCTCTT,CTCTCTCTT,T,CTCTCTCTCTCTT,CTCTT,CTCTCTCTCTT
Primary Allele: CSecondary Allele: CTCTCTT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTCATATAAGCAAATGTATATATTGTGTGACACAAATTTTTTTCAGTTTGAAACTTATTTTACTCAACCTCCATCCTCTCTCTCTCTCTCTCTCTCTCT[C/CTCTCTT,CTCTCTCTT,T,CTCTCTCTCTCTT,CTCTT,CTCTCTCTCTT]
TCACAAGAGAATTGTCATCAAATGTATTGATTCTTATGCATGCTATCTGAAAATTAATGTTATGTTCTCAGGTTCTGACCATTAACCAGTGGTACACATT

Reverse complement sequence

AATGTGTACCACTGGTTAATGGTCAGAACCTGAGAACATAACATTAATTTTCAGATAGCATGCATAAGAATCAATACATTTGATGACAATTCTCTTGTGA[G/AAGAGAG,AAGAGAGAG,A,AAGAGAGAGAGAG,AAGAG,AAGAGAGAGAG]
AGAGAGAGAGAGAGAGAGAGAGAGGATGGAGGTTGAGTAAAATAAGTTTCAAACTGAAAAAAATTTGTGTCACACAATATATACATTTGCTTATATGAGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CTCTCTT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.50% 22.00% 4.93% 23.85% CTCTCTCTT: 6.12%; T: 4.66%; CTCTT: 2.33%; CTCTCTCTCTT: 1.02%; CTCTCTCTCTCTT: 0.68%
All Indica  2759 3.40% 36.10% 6.92% 38.35% T: 6.27%; CTCTT: 3.62%; CTCTCTCTT: 3.59%; CTCTCTCTCTT: 1.09%; CTCTCTCTCTCTT: 0.62%
All Japonica  1512 94.20% 1.00% 0.60% 1.12% T: 2.71%; CTCTT: 0.13%; CTCTCTCTCTCTT: 0.13%; CTCTCTCTT: 0.07%
Aus  269 3.00% 3.70% 10.04% 13.75% CTCTCTCTT: 57.25%; CTCTCTCTCTT: 5.58%; CTCTCTCTCTCTT: 4.09%; CTCTT: 1.49%; T: 1.12%
Indica I  595 2.40% 15.50% 14.12% 53.11% CTCTT: 6.22%; CTCTCTCTT: 4.54%; T: 4.03%; CTCTCTCTCTT: 0.17%
Indica II  465 5.20% 34.20% 3.87% 41.94% T: 11.40%; CTCTCTCTT: 1.72%; CTCTT: 1.51%; CTCTCTCTCTCTT: 0.22%
Indica III  913 2.30% 52.00% 3.72% 26.40% T: 5.37%; CTCTCTCTT: 4.38%; CTCTT: 3.07%; CTCTCTCTCTCTT: 1.53%; CTCTCTCTCTT: 1.20%
Indica Intermediate  786 4.50% 34.50% 7.00% 38.93% T: 5.98%; CTCTT: 3.56%; CTCTCTCTT: 3.05%; CTCTCTCTCTT: 2.29%; CTCTCTCTCTCTT: 0.25%
Temperate Japonica  767 92.30% 0.40% 0.78% 1.43% T: 4.95%; CTCTT: 0.13%
Tropical Japonica  504 95.60% 2.20% 0.40% 0.60% T: 0.60%; CTCTCTCTCTCTT: 0.40%; CTCTT: 0.20%
Japonica Intermediate  241 97.50% 0.40% 0.41% 1.24% CTCTCTCTT: 0.41%
VI/Aromatic  96 54.20% 6.20% 4.17% 4.17% CTCTCTCTT: 28.12%; T: 1.04%; CTCTT: 1.04%; CTCTCTCTCTT: 1.04%
Intermediate  90 55.60% 11.10% 2.22% 12.22% CTCTCTCTT: 8.89%; CTCTT: 3.33%; T: 2.22%; CTCTCTCTCTCTT: 2.22%; CTCTCTCTCTT: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1209095184 C -> CTCTCTCTCTT LOC_Os12g15950.1 upstream_gene_variant ; 3723.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTCTT LOC_Os12g15960.1 upstream_gene_variant ; 2547.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTCTT LOC_Os12g15950-LOC_Os12g15960 intergenic_region ; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTCTCTT LOC_Os12g15950.1 upstream_gene_variant ; 3723.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTCTCTT LOC_Os12g15960.1 upstream_gene_variant ; 2547.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTCTCTT LOC_Os12g15950-LOC_Os12g15960 intergenic_region ; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTT LOC_Os12g15950.1 upstream_gene_variant ; 3723.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTT LOC_Os12g15960.1 upstream_gene_variant ; 2547.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTT LOC_Os12g15950-LOC_Os12g15960 intergenic_region ; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTT LOC_Os12g15950.1 upstream_gene_variant ; 3723.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTT LOC_Os12g15960.1 upstream_gene_variant ; 2547.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTCTT LOC_Os12g15950-LOC_Os12g15960 intergenic_region ; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> T LOC_Os12g15950.1 upstream_gene_variant ; 3722.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> T LOC_Os12g15960.1 upstream_gene_variant ; 2548.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> T LOC_Os12g15950-LOC_Os12g15960 intergenic_region ; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> DEL N N silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTT LOC_Os12g15950.1 upstream_gene_variant ; 3723.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTT LOC_Os12g15960.1 upstream_gene_variant ; 2547.0bp to feature; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N
vg1209095184 C -> CTCTCTT LOC_Os12g15950-LOC_Os12g15960 intergenic_region ; MODIFIER silent_mutation Average:56.352; most accessible tissue: Callus, score: 77.309 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209095184 NA 1.77E-25 mr1350_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
vg1209095184 NA 2.03E-06 mr1350_2 Ind_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