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Detailed information for vg0428960374:

Variant ID: vg0428960374 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 28960374
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCAAAGAGATTAGATGCAACTTCATCTTGTGCTTCCAAGCGGCATAATGTGTCCCATCAAAATGAGGTGCACGCCCGGAAGGCACGGAGACAAAGTTAT[G/T]
AGGAGGAACATTAAGTTTGATGTAATCAAAGTGAATAGTAGCTCCCTTTGATCCAGTCTCCTTGGTGCTAGAAGCGTCTCCCTTCTCCTCCAAATATTCG

Reverse complement sequence

CGAATATTTGGAGGAGAAGGGAGACGCTTCTAGCACCAAGGAGACTGGATCAAAGGGAGCTACTATTCACTTTGATTACATCAAACTTAATGTTCCTCCT[C/A]
ATAACTTTGTCTCCGTGCCTTCCGGGCGTGCACCTCATTTTGATGGGACACATTATGCCGCTTGGAAGCACAAGATGAAGTTGCATCTAATCTCTTTGCA

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 52.50% 1.60% 12.17% 33.75% NA
All Indica  2759 22.70% 2.60% 18.96% 55.74% NA
All Japonica  1512 99.60% 0.00% 0.07% 0.33% NA
Aus  269 71.00% 1.90% 16.36% 10.78% NA
Indica I  595 10.30% 2.20% 11.26% 76.30% NA
Indica II  465 10.80% 1.50% 12.26% 75.48% NA
Indica III  913 37.50% 2.80% 26.51% 33.19% NA
Indica Intermediate  786 22.10% 3.20% 19.97% 54.71% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 99.40% 0.00% 0.20% 0.40% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 96.90% 0.00% 0.00% 3.12% NA
Intermediate  90 68.90% 1.10% 7.78% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0428960374 G -> DEL LOC_Os04g48590.1 N frameshift_variant Average:14.581; most accessible tissue: Callus, score: 20.623 N N N N
vg0428960374 G -> T LOC_Os04g48590.1 missense_variant ; p.His41Asn; MODERATE nonsynonymous_codon ; H41N Average:14.581; most accessible tissue: Callus, score: 20.623 benign 1.278 TOLERATED 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0428960374 NA 2.34E-23 mr1083 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
vg0428960374 NA 9.97E-06 mr1104 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
vg0428960374 NA 1.75E-13 mr1169 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
vg0428960374 NA 1.26E-27 mr1181 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
vg0428960374 NA 4.34E-06 mr1181 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
vg0428960374 1.78E-06 1.24E-13 mr1195 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
vg0428960374 6.15E-06 3.00E-06 mr1448 Ind_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
vg0428960374 NA 4.77E-13 mr1655 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
vg0428960374 NA 4.86E-09 mr1770 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
vg0428960374 NA 3.64E-07 mr1804 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
vg0428960374 NA 3.26E-06 mr1970 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
vg0428960374 NA 4.54E-08 mr1973 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