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Detailed information for vg0602474331:

Variant ID: vg0602474331 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 2474331
Reference Allele: CAAlternative Allele: AA,CAA,C,CAAA
Primary Allele: CASecondary Allele: AA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCAAACCTTTATAATTCCATCTTTCTAGATTCATGCTCTCAATTTGTTTAGACAGAGGGCGTGATTTACAAGTCAATCCGTACAGACATTTTCTCTGT[CA/AA,CAA,C,CAAA]
AAAAAAAACCAAATTTCTTGAGATAATAAGCATATTTAGTTTGTGTTTTTTGAAGTTGGTTTTTTTAAACGGAGGATGTAATTTATATGCAACGGCACAT

Reverse complement sequence

ATGTGCCGTTGCATATAAATTACATCCTCCGTTTAAAAAAACCAACTTCAAAAAACACAAACTAAATATGCTTATTATCTCAAGAAATTTGGTTTTTTTT[TG/TT,TTG,G,TTTG]
ACAGAGAAAATGTCTGTACGGATTGACTTGTAAATCACGCCCTCTGTCTAAACAAATTGAGAGCATGAATCTAGAAAGATGGAATTATAAAGGTTTGGTT

Allele Frequencies:

Populations Population SizeFrequency of CA(primary allele) Frequency of AA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.10% 4.90% 2.88% 2.92% CAA: 1.84%; C: 0.34%; CAAA: 0.04%
All Indica  2759 93.30% 3.20% 1.56% 1.78% C: 0.07%; CAA: 0.07%
All Japonica  1512 88.90% 0.20% 4.76% 0.07% CAA: 5.56%; C: 0.40%; CAAA: 0.13%
Aus  269 9.70% 49.40% 6.69% 32.34% C: 1.86%
Indica I  595 97.30% 0.30% 1.51% 0.84% NA
Indica II  465 98.50% 0.40% 0.65% 0.22% C: 0.22%
Indica III  913 91.60% 4.90% 1.75% 1.53% CAA: 0.22%
Indica Intermediate  786 89.30% 5.00% 1.91% 3.69% C: 0.13%
Temperate Japonica  767 87.10% 0.10% 7.56% 0.00% CAA: 5.08%; CAAA: 0.13%
Tropical Japonica  504 88.10% 0.00% 2.18% 0.20% CAA: 8.13%; C: 1.19%; CAAA: 0.20%
Japonica Intermediate  241 96.30% 0.80% 1.24% 0.00% CAA: 1.66%
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 85.60% 5.60% 3.33% 1.11% C: 3.33%; CAA: 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
vg0602474331 CA -> CAAA LOC_Os06g05470.1 downstream_gene_variant ; 927.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> CAAA LOC_Os06g05480.1 downstream_gene_variant ; 3159.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> CAAA LOC_Os06g05470-LOC_Os06g05480 intergenic_region ; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> AA LOC_Os06g05470.1 downstream_gene_variant ; 925.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> AA LOC_Os06g05480.1 downstream_gene_variant ; 3161.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> AA LOC_Os06g05470-LOC_Os06g05480 intergenic_region ; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> DEL N N silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> CAA LOC_Os06g05470.1 downstream_gene_variant ; 927.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> CAA LOC_Os06g05480.1 downstream_gene_variant ; 3159.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> CAA LOC_Os06g05470-LOC_Os06g05480 intergenic_region ; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> C LOC_Os06g05470.1 downstream_gene_variant ; 926.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> C LOC_Os06g05480.1 downstream_gene_variant ; 3160.0bp to feature; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N
vg0602474331 CA -> C LOC_Os06g05470-LOC_Os06g05480 intergenic_region ; MODIFIER silent_mutation Average:58.643; most accessible tissue: Minghui63 root, score: 85.669 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602474331 3.36E-06 NA mr1141_2 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