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Detailed information for vg0604281708:

Variant ID: vg0604281708 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4281708
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATATATGAAAGAGGGTATTGCTTGAATCGTCCAATGGGTAGTCCTTAATAAATAGTTCCCTGCGTGTGTATTTGAGGCTGGTCTAGTAACTAGCCACAT[T/C]
TCAGTTTTGATATCTTTCTATCGATGACTCTATAAACTGTAAGTCTGTAACCCTCCTATTGAAAAAAAAGGTCTATTTGATTCAAAACTCCCATTCAATC

Reverse complement sequence

GATTGAATGGGAGTTTTGAATCAAATAGACCTTTTTTTTCAATAGGAGGGTTACAGACTTACAGTTTATAGAGTCATCGATAGAAAGATATCAAAACTGA[A/G]
ATGTGGCTAGTTACTAGACCAGCCTCAAATACACACGCAGGGAACTATTTATTAAGGACTACCCATTGGACGATTCAAGCAATACCCTCTTTCATATATG

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 89.30% 10.70% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 67.30% 32.70% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 45.20% 54.80% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0604281708 T -> C LOC_Os06g08610.1 upstream_gene_variant ; 5000.0bp to feature; MODIFIER silent_mutation Average:68.62; most accessible tissue: Callus, score: 85.664 N N N N
vg0604281708 T -> C LOC_Os06g08600.1 downstream_gene_variant ; 4568.0bp to feature; MODIFIER silent_mutation Average:68.62; most accessible tissue: Callus, score: 85.664 N N N N
vg0604281708 T -> C LOC_Os06g08600-LOC_Os06g08610 intergenic_region ; MODIFIER silent_mutation Average:68.62; most accessible tissue: Callus, score: 85.664 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604281708 1.86E-06 NA 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
vg0604281708 6.44E-12 1.02E-30 mr1115 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
vg0604281708 5.75E-08 5.01E-17 mr1115 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
vg0604281708 4.31E-21 5.55E-56 mr1137 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
vg0604281708 4.04E-11 1.86E-23 mr1137 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
vg0604281708 9.38E-08 2.07E-25 mr1611 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
vg0604281708 8.36E-06 5.60E-13 mr1611 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
vg0604281708 6.75E-21 1.13E-48 mr1617 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
vg0604281708 5.23E-12 7.29E-21 mr1617 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
vg0604281708 5.68E-11 1.99E-28 mr1920 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
vg0604281708 2.72E-07 1.25E-13 mr1920 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
vg0604281708 1.34E-12 2.93E-33 mr1115_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
vg0604281708 9.72E-09 2.02E-17 mr1115_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
vg0604281708 1.87E-30 1.37E-69 mr1137_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
vg0604281708 2.76E-15 4.34E-28 mr1137_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
vg0604281708 1.39E-07 NA mr1241_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
vg0604281708 5.93E-10 2.14E-28 mr1611_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
vg0604281708 2.98E-08 1.14E-15 mr1611_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
vg0604281708 7.40E-19 2.22E-44 mr1617_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
vg0604281708 2.80E-11 6.42E-18 mr1617_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