Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0607505388:

Variant ID: vg0607505388 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7505388
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTCACGCTAAAATTGAAAGTTTGGTTGAAATTGAAACGATGTGATAGAAAAGTTGAAAGTTTATGTGTGTAGAAAAGTTTTGATGTGATAGAAAAGTTA[G/A]
AAGTTTGAAGAAAAACTTTGAAACTAAACTCAGCCTGAATCTGAATAAATATCTGTTCAAGTCTGTTCGAAAAGTAGTTTTTTTAGATGGAGGGTACATA

Reverse complement sequence

TATGTACCCTCCATCTAAAAAAACTACTTTTCGAACAGACTTGAACAGATATTTATTCAGATTCAGGCTGAGTTTAGTTTCAAAGTTTTTCTTCAAACTT[C/T]
TAACTTTTCTATCACATCAAAACTTTTCTACACACATAAACTTTCAACTTTTCTATCACATCGTTTCAATTTCAACCAAACTTTCAATTTTAGCGTGAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.70% 5.30% 0.02% 0.00% NA
All Indica  2759 94.10% 5.90% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 82.20% 17.80% 0.00% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 93.90% 6.10% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 26.00% 74.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0607505388 G -> A LOC_Os06g13580.1 upstream_gene_variant ; 4871.0bp to feature; MODIFIER silent_mutation Average:40.54; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0607505388 G -> A LOC_Os06g13580-LOC_Os06g13590 intergenic_region ; MODIFIER silent_mutation Average:40.54; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607505388 7.05E-06 NA mr1128_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
vg0607505388 2.83E-06 2.83E-06 mr1367_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
vg0607505388 NA 1.71E-07 mr1405_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
vg0607505388 2.97E-07 2.73E-10 mr1547_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
vg0607505388 NA 4.68E-07 mr1547_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
vg0607505388 NA 9.31E-07 mr1567_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
vg0607505388 NA 6.42E-06 mr1597_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