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Detailed information for vg0524582362:

Variant ID: vg0524582362 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 24582362
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCCGTTTCAAAATATTTGACACCGTTGACTTTTTAGCACATATTTGACCGTTCATCTTATTTAAAAATTTTTGTGAAATATGTAAAACTATTTGTGTA[C/T]
ATGAAAGTATATTTAACAATAAATCAAATGATGTGAAAAGAATAAATAATTACTTTAATTTTTTGAATAAAACGAATGATTAAACACGTACTAAAAAGTC

Reverse complement sequence

GACTTTTTAGTACGTGTTTAATCATTCGTTTTATTCAAAAAATTAAAGTAATTATTTATTCTTTTCACATCATTTGATTTATTGTTAAATATACTTTCAT[G/A]
TACACAAATAGTTTTACATATTTCACAAAAATTTTTAAATAAGATGAACGGTCAAATATGTGCTAAAAAGTCAACGGTGTCAAATATTTTGAAACGGAGG

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 94.60% 5.40% 0.00% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 24.50% 75.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0524582362 C -> T LOC_Os05g41970.1 upstream_gene_variant ; 4626.0bp to feature; MODIFIER silent_mutation Average:40.308; most accessible tissue: Minghui63 root, score: 67.73 N N N N
vg0524582362 C -> T LOC_Os05g41990.1 upstream_gene_variant ; 888.0bp to feature; MODIFIER silent_mutation Average:40.308; most accessible tissue: Minghui63 root, score: 67.73 N N N N
vg0524582362 C -> T LOC_Os05g42000.1 upstream_gene_variant ; 4783.0bp to feature; MODIFIER silent_mutation Average:40.308; most accessible tissue: Minghui63 root, score: 67.73 N N N N
vg0524582362 C -> T LOC_Os05g42000.2 upstream_gene_variant ; 4783.0bp to feature; MODIFIER silent_mutation Average:40.308; most accessible tissue: Minghui63 root, score: 67.73 N N N N
vg0524582362 C -> T LOC_Os05g41980.1 downstream_gene_variant ; 2687.0bp to feature; MODIFIER silent_mutation Average:40.308; most accessible tissue: Minghui63 root, score: 67.73 N N N N
vg0524582362 C -> T LOC_Os05g41980-LOC_Os05g41990 intergenic_region ; MODIFIER silent_mutation Average:40.308; most accessible tissue: Minghui63 root, score: 67.73 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0524582362 NA 6.38E-06 mr1373 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
vg0524582362 NA 1.22E-08 mr1465 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
vg0524582362 NA 2.60E-11 mr1499 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
vg0524582362 3.46E-09 1.43E-19 mr1612 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
vg0524582362 NA 9.61E-06 mr1684 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
vg0524582362 NA 4.16E-07 mr1706 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
vg0524582362 3.94E-06 NA mr1935 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
vg0524582362 NA 2.92E-08 mr1989 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
vg0524582362 2.55E-07 NA mr1109_2 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
vg0524582362 NA 8.60E-17 mr1119_2 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
vg0524582362 NA 4.03E-08 mr1126_2 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
vg0524582362 NA 3.04E-10 mr1166_2 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
vg0524582362 1.13E-09 2.23E-16 mr1612_2 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
vg0524582362 NA 2.09E-06 mr1815_2 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
vg0524582362 7.85E-06 NA mr1896_2 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