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Detailed information for vg0824546058:

Variant ID: vg0824546058 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24546058
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTTTAAATCATAGGAATGAAAAAACAGAGGAATAGGAAAAATATAGGATTCTGATAGGAATACAAGTGTAAAACAGAGGAATGCAAAACACAGGAAAAA[C/T]
ATAGAAATGACCGTTTGATTGAGCCGCAGGAAAAACACAGGAATTTGATAAGAGATAAAGACTCAGGGCTTATTCGGAATGCAGGATTGAAAAAATATAG

Reverse complement sequence

CTATATTTTTTCAATCCTGCATTCCGAATAAGCCCTGAGTCTTTATCTCTTATCAAATTCCTGTGTTTTTCCTGCGGCTCAATCAAACGGTCATTTCTAT[G/A]
TTTTTCCTGTGTTTTGCATTCCTCTGTTTTACACTTGTATTCCTATCAGAATCCTATATTTTTCCTATTCCTCTGTTTTTTCATTCCTATGATTTAAAGG

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 97.10% 1.70% 1.18% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 91.10% 5.20% 3.64% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 84.00% 9.40% 6.65% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 95.90% 2.90% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 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
vg0824546058 C -> T LOC_Os08g38820.1 upstream_gene_variant ; 3885.0bp to feature; MODIFIER silent_mutation Average:29.848; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0824546058 C -> T LOC_Os08g38840.1 upstream_gene_variant ; 1958.0bp to feature; MODIFIER silent_mutation Average:29.848; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0824546058 C -> T LOC_Os08g38820.2 upstream_gene_variant ; 3885.0bp to feature; MODIFIER silent_mutation Average:29.848; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0824546058 C -> T LOC_Os08g38830.1 downstream_gene_variant ; 927.0bp to feature; MODIFIER silent_mutation Average:29.848; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0824546058 C -> T LOC_Os08g38830-LOC_Os08g38840 intergenic_region ; MODIFIER silent_mutation Average:29.848; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824546058 NA 2.45E-07 mr1305_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
vg0824546058 3.08E-06 3.08E-06 mr1430_2 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
vg0824546058 NA 3.38E-07 mr1585_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
vg0824546058 NA 4.90E-08 mr1765_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