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Detailed information for vg0625083670:

Variant ID: vg0625083670 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25083670
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACACTAAACAATATAAAAAAAATCTCAACAACAAGATCAAGTAAAACACTCCAGTACTAAATTATTATTGGCCACGGGAGCATATCCTATGCACACAGG[C/A,T]
CCTCGCGTGTACACACCGTGTACACCAACTAAAAATTATCACAAAAAATTCTAGGAAAATTCATACATGTATTTTCAATAGTATTACATCTACGTATAAA

Reverse complement sequence

TTTATACGTAGATGTAATACTATTGAAAATACATGTATGAATTTTCCTAGAATTTTTTGTGATAATTTTTAGTTGGTGTACACGGTGTGTACACGCGAGG[G/T,A]
CCTGTGTGCATAGGATATGCTCCCGTGGCCAATAATAATTTAGTACTGGAGTGTTTTACTTGATCTTGTTGTTGAGATTTTTTTTATATTGTTTAGTGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.10% 0.72% 0.00% T: 0.08%
All Indica  2759 99.80% 0.00% 0.04% 0.00% T: 0.14%
All Japonica  1512 94.40% 3.50% 2.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.00% 0.00% T: 0.22%
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.00% 0.13% 0.00% T: 0.38%
Temperate Japonica  767 89.00% 6.90% 4.04% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% 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
vg0625083670 C -> T LOC_Os06g41820.1 upstream_gene_variant ; 1740.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> T LOC_Os06g41830.1 upstream_gene_variant ; 1867.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> T LOC_Os06g41840.1 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> T LOC_Os06g41840.2 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> T LOC_Os06g41840.3 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> T LOC_Os06g41840.4 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> T LOC_Os06g41820-LOC_Os06g41830 intergenic_region ; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> A LOC_Os06g41820.1 upstream_gene_variant ; 1740.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> A LOC_Os06g41830.1 upstream_gene_variant ; 1867.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> A LOC_Os06g41840.1 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> A LOC_Os06g41840.2 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> A LOC_Os06g41840.3 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> A LOC_Os06g41840.4 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0625083670 C -> A LOC_Os06g41820-LOC_Os06g41830 intergenic_region ; MODIFIER silent_mutation Average:43.032; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625083670 4.13E-06 4.13E-06 mr1456 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