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Detailed information for vg0104576190:

Variant ID: vg0104576190 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4576190
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGCAAGGCTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGCCATGTCGACAACAGTTTGATAAGCTACCCACATATTGTACTGGTGTTATTATG[G/T,A]
TGAATAAAAGCAACTCCGGCTCCGGCCAACAGGATGTAGGGTTATTACCTGACAATTTAGGGGCCCGAACCTGTATAAAAATCCTCGTCTCCATCTCTTT

Reverse complement sequence

AAAGAGATGGAGACGAGGATTTTTATACAGGTTCGGGCCCCTAAATTGTCAGGTAATAACCCTACATCCTGTTGGCCGGAGCCGGAGTTGCTTTTATTCA[C/A,T]
CATAATAACACCAGTACAATATGTGGGTAGCTTATCAAACTGTTGTCGACATGGCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGCCTTGCTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.10% 3.30% 1.04% 0.57% NA
All Indica  2759 94.40% 5.50% 0.04% 0.00% NA
All Japonica  1512 95.40% 0.10% 2.98% 1.52% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 88.00% 11.90% 0.11% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 91.80% 0.00% 5.35% 2.87% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 0.00% 1.66% 0.41% NA
VI/Aromatic  96 93.80% 0.00% 2.08% 4.17% NA
Intermediate  90 98.90% 0.00% 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
vg0104576190 G -> T LOC_Os01g09100.1 upstream_gene_variant ; 2781.0bp to feature; MODIFIER N Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> T LOC_Os01g09090.1 downstream_gene_variant ; 3972.0bp to feature; MODIFIER N Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> T LOC_Os01g09110.1 downstream_gene_variant ; 35.0bp to feature; MODIFIER N Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> T LOC_Os01g09120.1 downstream_gene_variant ; 4958.0bp to feature; MODIFIER N Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> T LOC_Os01g09120.2 downstream_gene_variant ; 4958.0bp to feature; MODIFIER N Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> T LOC_Os01g09110-LOC_Os01g09120 intergenic_region ; MODIFIER N Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> A LOC_Os01g09100.1 upstream_gene_variant ; 2781.0bp to feature; MODIFIER silent_mutation Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> A LOC_Os01g09090.1 downstream_gene_variant ; 3972.0bp to feature; MODIFIER silent_mutation Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> A LOC_Os01g09110.1 downstream_gene_variant ; 35.0bp to feature; MODIFIER silent_mutation Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> A LOC_Os01g09120.1 downstream_gene_variant ; 4958.0bp to feature; MODIFIER silent_mutation Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> A LOC_Os01g09120.2 downstream_gene_variant ; 4958.0bp to feature; MODIFIER silent_mutation Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> A LOC_Os01g09110-LOC_Os01g09120 intergenic_region ; MODIFIER silent_mutation Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0104576190 G -> DEL N N silent_mutation Average:57.504; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104576190 5.12E-07 5.12E-07 mr1915 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
vg0104576190 NA 6.63E-06 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
vg0104576190 NA 4.66E-08 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