Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0619983787:

Variant ID: vg0619983787 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19983787
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTCTGTTGGGAAATTTTGACCTCTCGGCATGGATCGCGCACGGTTATTCCCATCCGTTGCATGCACTATCAACGTGATTAATTCACCTAGTGTTAATTT[C/A]
TGTAATTACACATTATGCGTATTTTTTTTAGAATTCATCCTGTAGATTGACGAAGTCACCACATGCGCCTCGCTATTGACGGATGTACGTCGCCTTCCAT

Reverse complement sequence

ATGGAAGGCGACGTACATCCGTCAATAGCGAGGCGCATGTGGTGACTTCGTCAATCTACAGGATGAATTCTAAAAAAAATACGCATAATGTGTAATTACA[G/T]
AAATTAACACTAGGTGAATTAATCACGTTGATAGTGCATGCAACGGATGGGAATAACCGTGCGCGATCCATGCCGAGAGGTCAAAATTTCCCAACAGAAC

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 92.50% 7.40% 0.11% 0.00% NA
All Indica  2759 88.30% 11.60% 0.14% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 80.70% 19.10% 0.22% 0.00% NA
Indica Intermediate  786 87.00% 12.70% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0619983787 C -> A LOC_Os06g34340.1 upstream_gene_variant ; 1911.0bp to feature; MODIFIER silent_mutation Average:67.311; most accessible tissue: Minghui63 root, score: 86.438 N N N N
vg0619983787 C -> A LOC_Os06g34340-LOC_Os06g34350 intergenic_region ; MODIFIER silent_mutation Average:67.311; most accessible tissue: Minghui63 root, score: 86.438 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619983787 NA 1.88E-06 mr1798 Ind_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
vg0619983787 NA 3.55E-06 mr1037_2 Ind_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
vg0619983787 NA 3.28E-07 mr1458_2 Ind_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
vg0619983787 2.98E-07 1.64E-10 mr1798_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