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Detailed information for vg0135088154:

Variant ID: vg0135088154 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 35088154
Reference Allele: GAlternative Allele: GACATAT,T,GAATGAATCTAGACATAT
Primary Allele: GACATATSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 34. )

Flanking Sequence (100 bp) in Reference Genome:


AAAACAAACTTAGAATAAGACTTCTTTCTCATCTATAGTACTCCCTCCATTTCATAATGTAAGATTTTCTAGCATTGCTCATATATATATATAATGTTTA[G/GACATAT,T,GAATGAATCTAGACATAT]
ATAATGTTTAGATTCATTAGCATCTATATGAATGTAAGCAATGCTAGAAAGTCTTACAATGTGAAACGGAGGAAGTAGTGACTAGTCTCTTTATATTTGA

Reverse complement sequence

TCAAATATAAAGAGACTAGTCACTACTTCCTCCGTTTCACATTGTAAGACTTTCTAGCATTGCTTACATTCATATAGATGCTAATGAATCTAAACATTAT[C/ATATGTC,A,ATATGTCTAGATTCATTC]
TAAACATTATATATATATATGAGCAATGCTAGAAAATCTTACATTATGAAATGGAGGGAGTACTATAGATGAGAAAGAAGTCTTATTCTAAGTTTGTTTT

Allele Frequencies:

Populations Population SizeFrequency of GACATAT(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.10% 28.60% 16.08% 17.14% T: 0.99%; GAATGAATCTAGACATAT: 0.04%
All Indica  2759 44.20% 2.50% 25.73% 26.57% T: 0.98%; GAATGAATCTAGACATAT: 0.04%
All Japonica  1512 22.00% 75.50% 1.19% 0.46% T: 0.79%
Aus  269 64.30% 4.10% 7.43% 21.93% T: 2.23%
Indica I  595 34.30% 4.20% 46.89% 13.95% T: 0.67%
Indica II  465 28.60% 0.90% 35.48% 34.19% T: 0.65%; GAATGAATCTAGACATAT: 0.22%
Indica III  913 57.70% 0.30% 9.42% 31.33% T: 1.20%
Indica Intermediate  786 45.30% 4.60% 22.90% 26.08% T: 1.15%
Temperate Japonica  767 1.60% 97.10% 0.65% 0.52% T: 0.13%
Tropical Japonica  504 46.80% 49.60% 1.79% 0.60% T: 1.19%
Japonica Intermediate  241 35.30% 61.00% 1.66% 0.00% T: 2.07%
VI/Aromatic  96 4.20% 93.80% 1.04% 1.04% NA
Intermediate  90 27.80% 45.60% 12.22% 11.11% T: 2.22%; GAATGAATCTAGACATAT: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135088154 G -> GAATGAATCTAGACATAT LOC_Os01g60670.1 upstream_gene_variant ; 2567.0bp to feature; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> GAATGAATCTAGACATAT LOC_Os01g60680.1 downstream_gene_variant ; 746.0bp to feature; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> GAATGAATCTAGACATAT LOC_Os01g60670-LOC_Os01g60680 intergenic_region ; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> T LOC_Os01g60670.1 upstream_gene_variant ; 2566.0bp to feature; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> T LOC_Os01g60680.1 downstream_gene_variant ; 747.0bp to feature; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> T LOC_Os01g60670-LOC_Os01g60680 intergenic_region ; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> GACATAT LOC_Os01g60670.1 upstream_gene_variant ; 2567.0bp to feature; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> GACATAT LOC_Os01g60680.1 downstream_gene_variant ; 746.0bp to feature; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> GACATAT LOC_Os01g60670-LOC_Os01g60680 intergenic_region ; MODIFIER silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0135088154 G -> DEL N N silent_mutation Average:35.768; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135088154 1.14E-06 NA mr1889 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