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Detailed information for vg0401333600:

Variant ID: vg0401333600 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1333600
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAGAACAAGAGGGAAAAAAAGGTGGGGCAGTGGAGGTGCCTAATATTAGTGATTCCATTGGGTGACCCTTGGAAAGCATTTTTCTTATTTATTAATCAG[G/A]
TAAGATGATCAAGCGTTCATTGGCTAGCATGGGAAAACCCAGATAAAACTGAAGCCACACATTTATGTGGGATCAATTTCTCTATAACGGATGATTTTCT

Reverse complement sequence

AGAAAATCATCCGTTATAGAGAAATTGATCCCACATAAATGTGTGGCTTCAGTTTTATCTGGGTTTTCCCATGCTAGCCAATGAACGCTTGATCATCTTA[C/T]
CTGATTAATAAATAAGAAAAATGCTTTCCAAGGGTCACCCAATGGAATCACTAATATTAGGCACCTCCACTGCCCCACCTTTTTTTCCCTCTTGTTCTCC

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 73.40% 26.30% 0.30% 0.00% NA
All Indica  2759 64.80% 34.70% 0.47% 0.00% NA
All Japonica  1512 99.60% 0.30% 0.07% 0.00% NA
Aus  269 7.80% 92.20% 0.00% 0.00% NA
Indica I  595 76.10% 23.70% 0.17% 0.00% NA
Indica II  465 58.50% 41.50% 0.00% 0.00% NA
Indica III  913 63.10% 35.80% 1.10% 0.00% NA
Indica Intermediate  786 62.00% 37.80% 0.25% 0.00% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0401333600 G -> A LOC_Os04g03180.1 intron_variant ; MODIFIER silent_mutation Average:43.759; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401333600 NA 3.56E-06 mr1007 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
vg0401333600 3.92E-06 3.92E-06 mr1396 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
vg0401333600 NA 2.07E-08 mr1565 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
vg0401333600 NA 8.93E-08 mr1659 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
vg0401333600 NA 2.89E-07 mr1715 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
vg0401333600 NA 4.29E-13 mr1846_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