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Detailed information for vg0401805850:

Variant ID: vg0401805850 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1805850
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAATCATATAGTCGGGGGCTACACCTAATTAGGTGCATCTATTCGATGCACCATGTTTTTTATTTTTCGCCCTTTACAGTCTTCGTCTTCGCTACTCGG[C/A,T]
AGGCCTTAGCAGGAAAAATTAAAGCACTCGGATTATTATTTTTTGAGAGAGCTATGTTGTCGACTGCAAAGGTCTCGGGGGCTACTGTGGAGATTATGGA

Reverse complement sequence

TCCATAATCTCCACAGTAGCCCCCGAGACCTTTGCAGTCGACAACATAGCTCTCTCAAAAAATAATAATCCGAGTGCTTTAATTTTTCCTGCTAAGGCCT[G/T,A]
CCGAGTAGCGAAGACGAAGACTGTAAAGGGCGAAAAATAAAAAACATGGTGCATCGAATAGATGCACCTAATTAGGTGTAGCCCCCGACTATATGATTAG

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 89.20% 1.00% 2.01% 7.66% T: 0.08%
All Indica  2759 83.70% 1.30% 2.79% 12.11% T: 0.11%
All Japonica  1512 98.50% 0.10% 0.26% 1.19% NA
Aus  269 92.20% 3.00% 4.46% 0.37% NA
Indica I  595 85.40% 1.00% 2.86% 10.76% NA
Indica II  465 79.80% 0.20% 0.86% 18.92% T: 0.22%
Indica III  913 81.90% 2.50% 4.16% 11.28% T: 0.11%
Indica Intermediate  786 86.80% 0.80% 2.29% 10.05% T: 0.13%
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 96.60% 0.00% 0.40% 2.98% NA
Japonica Intermediate  241 98.30% 0.40% 0.83% 0.41% NA
VI/Aromatic  96 95.80% 2.10% 2.08% 0.00% NA
Intermediate  90 86.70% 2.20% 0.00% 10.00% T: 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
vg0401805850 C -> DEL N N silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> A LOC_Os04g03950.1 upstream_gene_variant ; 929.0bp to feature; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> A LOC_Os04g03970.1 upstream_gene_variant ; 2619.0bp to feature; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> A LOC_Os04g03960.1 downstream_gene_variant ; 659.0bp to feature; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> A LOC_Os04g03950-LOC_Os04g03960 intergenic_region ; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> T LOC_Os04g03950.1 upstream_gene_variant ; 929.0bp to feature; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> T LOC_Os04g03970.1 upstream_gene_variant ; 2619.0bp to feature; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> T LOC_Os04g03960.1 downstream_gene_variant ; 659.0bp to feature; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N
vg0401805850 C -> T LOC_Os04g03950-LOC_Os04g03960 intergenic_region ; MODIFIER silent_mutation Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401805850 2.08E-06 NA mr1075_2 Ind_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