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Detailed information for vg0628339348:

Variant ID: vg0628339348 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28339348
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCAACCGAGACTAAAAATCATCTTTACTCCCGGTTCATCCCGTGTCAGTAGTTTGTCAGGGGGGCGATGATCTTTAGTCCCGGTTGGTGACATCAACC[G/T]
GGACTAAAGATCATCTTTATAGTCATCTTTATAGTCCCGGTTGATAATACTAACCAGGACTAAAAATTATATTGATCTTTAGTCCCGGTTAGTATTACCA

Reverse complement sequence

TGGTAATACTAACCGGGACTAAAGATCAATATAATTTTTAGTCCTGGTTAGTATTATCAACCGGGACTATAAAGATGACTATAAAGATGATCTTTAGTCC[C/A]
GGTTGATGTCACCAACCGGGACTAAAGATCATCGCCCCCCTGACAAACTACTGACACGGGATGAACCGGGAGTAAAGATGATTTTTAGTCTCGGTTGGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.30% 9.20% 1.52% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 67.20% 28.00% 4.76% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 56.50% 36.20% 7.30% 0.00% NA
Tropical Japonica  504 90.70% 8.70% 0.60% 0.00% NA
Japonica Intermediate  241 52.30% 42.30% 5.39% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0628339348 G -> T LOC_Os06g46650.1 upstream_gene_variant ; 2466.0bp to feature; MODIFIER silent_mutation Average:42.764; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N
vg0628339348 G -> T LOC_Os06g46650-LOC_Os06g46670 intergenic_region ; MODIFIER silent_mutation Average:42.764; most accessible tissue: Minghui63 young leaf, score: 61.887 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628339348 4.89E-06 NA mr1210 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
vg0628339348 NA 7.69E-06 mr1210 Jap_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
vg0628339348 2.47E-07 NA mr1585 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
vg0628339348 NA 4.67E-09 mr1585 Jap_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
vg0628339348 6.29E-09 NA mr1586 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
vg0628339348 NA 3.87E-07 mr1586 Jap_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
vg0628339348 5.84E-06 NA mr1305_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
vg0628339348 4.86E-06 NA mr1585_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
vg0628339348 NA 6.83E-07 mr1585_2 Jap_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