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Detailed information for vg0614481201:

Variant ID: vg0614481201 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14481201
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTGCTTATGCTAAACATAGTTTACATAAATTTCTCCATGATTTCATCTTGCATAGATTATTTTAAAGAATTAGAATAACCTTTCTTTGTATATGTGTTC[C/A]
TACTTCATAATTGCACCTAATATTATTATAGGGTTTACATTAAACTTCTTTTGGGCTGAGAAAATGATATTAGAATTTAATATTAAATCCACATGTTATC

Reverse complement sequence

GATAACATGTGGATTTAATATTAAATTCTAATATCATTTTCTCAGCCCAAAAGAAGTTTAATGTAAACCCTATAATAATATTAGGTGCAATTATGAAGTA[G/T]
GAACACATATACAAAGAAAGGTTATTCTAATTCTTTAAAATAATCTATGCAAGATGAAATCATGGAGAAATTTATGTAAACTATGTTTAGCATAAGCAGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.10% 7.00% 1.88% 28.02% NA
All Indica  2759 54.70% 1.00% 1.99% 42.33% NA
All Japonica  1512 72.00% 19.20% 1.65% 7.14% NA
Aus  269 84.40% 0.70% 1.12% 13.75% NA
Indica I  595 88.20% 0.00% 1.68% 10.08% NA
Indica II  465 74.80% 0.90% 2.37% 21.94% NA
Indica III  913 17.30% 0.40% 0.77% 81.49% NA
Indica Intermediate  786 60.80% 2.40% 3.44% 33.33% NA
Temperate Japonica  767 96.10% 1.40% 0.78% 1.69% NA
Tropical Japonica  504 30.60% 51.00% 2.38% 16.07% NA
Japonica Intermediate  241 82.20% 9.10% 2.90% 5.81% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 66.70% 14.40% 6.67% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0614481201 C -> A LOC_Os06g24660.1 upstream_gene_variant ; 2483.0bp to feature; MODIFIER silent_mutation Average:16.822; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N
vg0614481201 C -> A LOC_Os06g24650-LOC_Os06g24660 intergenic_region ; MODIFIER silent_mutation Average:16.822; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N
vg0614481201 C -> DEL N N silent_mutation Average:16.822; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614481201 7.57E-11 4.79E-24 mr1301 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
vg0614481201 5.45E-07 1.61E-15 mr1301 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
vg0614481201 2.10E-09 1.91E-18 mr1410 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
vg0614481201 2.83E-06 3.73E-16 mr1410 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
vg0614481201 NA 2.56E-08 mr1993 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
vg0614481201 NA 7.78E-07 mr1206_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
vg0614481201 7.86E-06 NA mr1301_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
vg0614481201 2.31E-07 2.06E-16 mr1410_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
vg0614481201 NA 1.08E-13 mr1410_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
vg0614481201 NA 4.58E-07 mr1668_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
vg0614481201 NA 2.21E-08 mr1786_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