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Detailed information for vg0619710671:

Variant ID: vg0619710671 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19710671
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTATAAATACACACACATACATGCATACCTATCCCTATAAATACACAACATACACCCCTACCCCTATGAAAATCTTCGAGAGATTGGACCGGCACATCTT[G/A]
ATATATTTTGAGATTAATTAAGTCACCATAAATATCTCTGTCAACGAGTAAACCTACCACTGATAAAATAATTAGCCGTAAAATACGAGATCACCCATGT

Reverse complement sequence

ACATGGGTGATCTCGTATTTTACGGCTAATTATTTTATCAGTGGTAGGTTTACTCGTTGACAGAGATATTTATGGTGACTTAATTAATCTCAAAATATAT[C/T]
AAGATGTGCCGGTCCAATCTCTCGAAGATTTTCATAGGGGTAGGGGTGTATGTTGTGTATTTATAGGGATAGGTATGCATGTATGTGTGTGTATTTATAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.70% 35.10% 0.15% 0.00% NA
All Indica  2759 96.50% 3.30% 0.18% 0.00% NA
All Japonica  1512 5.60% 94.40% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 97.50% 2.20% 0.34% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 98.80% 1.10% 0.11% 0.00% NA
Indica Intermediate  786 93.40% 6.40% 0.25% 0.00% NA
Temperate Japonica  767 3.40% 96.60% 0.00% 0.00% NA
Tropical Japonica  504 10.70% 89.30% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 44.40% 53.30% 2.22% 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
vg0619710671 G -> A LOC_Os06g33890.1 upstream_gene_variant ; 1826.0bp to feature; MODIFIER silent_mutation Average:52.655; most accessible tissue: Minghui63 young leaf, score: 64.378 N N N N
vg0619710671 G -> A LOC_Os06g33880-LOC_Os06g33890 intergenic_region ; MODIFIER silent_mutation Average:52.655; most accessible tissue: Minghui63 young leaf, score: 64.378 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619710671 2.00E-13 1.58E-83 mr1033 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
vg0619710671 NA 1.65E-26 mr1072 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
vg0619710671 NA 6.51E-50 mr1154 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
vg0619710671 1.18E-10 2.64E-48 mr1176 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
vg0619710671 NA 2.11E-06 mr1278 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
vg0619710671 NA 2.30E-29 mr1333 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
vg0619710671 9.05E-06 8.22E-73 mr1536 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
vg0619710671 NA 1.86E-26 mr1686 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
vg0619710671 NA 2.15E-07 mr1824 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
vg0619710671 NA 1.95E-69 mr1865 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
vg0619710671 2.93E-16 1.39E-114 mr1033_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
vg0619710671 NA 6.92E-96 mr1536_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