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Detailed information for vg0428508285:

Variant ID: vg0428508285 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 28508285
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTCCCGTGCACCGAGTCACTGACTCGTGGGCCCGCCCCAGGACCCCGCACGATGGATCCGGGTCTCCCTCTCTCTCTCCCCGCCTCCCTCTGTTGGAC[C/T]
GCCTACTTAGGCCGCGTCGGCCCAATTAATTGGCCGAGCCGCGCCAACTCCTCTCGGGCCGCGCTCAAGCCGCCCGCGAAGTCTACATCTCCTCCCTATC

Reverse complement sequence

GATAGGGAGGAGATGTAGACTTCGCGGGCGGCTTGAGCGCGGCCCGAGAGGAGTTGGCGCGGCTCGGCCAATTAATTGGGCCGACGCGGCCTAAGTAGGC[G/A]
GTCCAACAGAGGGAGGCGGGGAGAGAGAGAGGGAGACCCGGATCCATCGTGCGGGGTCCTGGGGCGGGCCCACGAGTCAGTGACTCGGTGCACGGGAGAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 1.90% 0.49% 0.00% NA
All Indica  2759 98.70% 1.20% 0.07% 0.00% NA
All Japonica  1512 95.40% 3.20% 1.39% 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 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.25% 0.00% NA
Temperate Japonica  767 93.10% 4.30% 2.61% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.40% 0.41% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 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
vg0428508285 C -> T LOC_Os04g47940.1 upstream_gene_variant ; 988.0bp to feature; MODIFIER silent_mutation Average:53.402; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0428508285 C -> T LOC_Os04g47940-LOC_Os04g47950 intergenic_region ; MODIFIER silent_mutation Average:53.402; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0428508285 NA 1.95E-10 Awn_length Jap_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
vg0428508285 NA 6.76E-06 mr1382 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
vg0428508285 NA 1.94E-06 mr1038_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
vg0428508285 NA 5.28E-07 mr1057_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
vg0428508285 2.39E-06 2.39E-06 mr1681_2 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