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Detailed information for vg0430790041:

Variant ID: vg0430790041 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30790041
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAGGGGGAAAAATTAATCAGGCATGAAGCTAATATCAAAGGGCAAATTAATCTAGCTAGCTACTACAGCTAGCACCAGCATGAGCAAATATACAACAGG[G/A]
TTGCATTAACTGATCGATCAGCTAGCTCCCCTCATGGTGATCATAGAGATGACGACGAAGACGCAGTGTGGATCGATATGAAGGAGAGATCAGCTTGCAG

Reverse complement sequence

CTGCAAGCTGATCTCTCCTTCATATCGATCCACACTGCGTCTTCGTCGTCATCTCTATGATCACCATGAGGGGAGCTAGCTGATCGATCAGTTAATGCAA[C/T]
CCTGTTGTATATTTGCTCATGCTGGTGCTAGCTGTAGTAGCTAGCTAGATTAATTTGCCCTTTGATATTAGCTTCATGCCTGATTAATTTTTCCCCCTTT

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 95.20% 4.80% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 85.30% 14.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 72.80% 27.20% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0430790041 G -> A LOC_Os04g51900.1 upstream_gene_variant ; 1775.0bp to feature; MODIFIER silent_mutation Average:54.29; most accessible tissue: Callus, score: 83.167 N N N N
vg0430790041 G -> A LOC_Os04g51890-LOC_Os04g51900 intergenic_region ; MODIFIER silent_mutation Average:54.29; most accessible tissue: Callus, score: 83.167 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430790041 NA 3.59E-19 Awn_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0430790041 9.86E-06 NA mr1609 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
vg0430790041 8.56E-07 8.56E-07 mr1609 Jap_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
vg0430790041 6.92E-06 NA mr1841 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
vg0430790041 2.99E-06 NA mr1900 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
vg0430790041 NA 2.26E-06 mr1900 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