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Detailed information for vg0614462540:

Variant ID: vg0614462540 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14462540
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTGGTTTCCTCGCCCGTGTTAATCTTACTGGATACTCGCAAGGACTTCTTGGTGTACTGTGACGCTTCGCGCCAAGGATTGGGGTGTGTATTAATGCA[G/A]
GAAGGTCATGTGGTAGCCTATGCCTCACGCCAGCTACGGCCCCATGAAGGCAACTATCCTACTCATGATTTGGAGTTGGCCGCTGTGGTTCATGATTTGA

Reverse complement sequence

TCAAATCATGAACCACAGCGGCCAACTCCAAATCATGAGTAGGATAGTTGCCTTCATGGGGCCGTAGCTGGCGTGAGGCATAGGCTACCACATGACCTTC[C/T]
TGCATTAATACACACCCCAATCCTTGGCGCGAAGCGTCACAGTACACCAAGAAGTCCTTGCGAGTATCCAGTAAGATTAACACGGGCGAGGAAACCAGCT

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 36.90% 4.50% 12.25% 46.32% NA
All Indica  2759 7.90% 0.70% 20.70% 70.68% NA
All Japonica  1512 91.70% 0.10% 0.13% 8.13% NA
Aus  269 3.70% 68.40% 0.74% 27.14% NA
Indica I  595 12.10% 0.00% 5.38% 82.52% NA
Indica II  465 5.20% 0.20% 11.83% 82.80% NA
Indica III  913 3.20% 0.40% 34.94% 61.45% NA
Indica Intermediate  786 12.00% 1.80% 20.99% 65.27% NA
Temperate Japonica  767 96.90% 0.00% 0.00% 3.13% NA
Tropical Japonica  504 82.90% 0.20% 0.40% 16.47% NA
Japonica Intermediate  241 93.40% 0.00% 0.00% 6.64% NA
VI/Aromatic  96 85.40% 4.20% 0.00% 10.42% NA
Intermediate  90 51.10% 7.80% 4.44% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0614462540 G -> A LOC_Os06g24630.1 synonymous_variant ; p.Gln558Gln; LOW synonymous_codon Average:15.357; most accessible tissue: Callus, score: 25.601 N N N N
vg0614462540 G -> DEL LOC_Os06g24630.1 N frameshift_variant Average:15.357; most accessible tissue: Callus, score: 25.601 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614462540 NA 4.07E-06 mr1403 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
vg0614462540 NA 9.24E-06 mr1608 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
vg0614462540 NA 3.65E-16 mr1830 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
vg0614462540 NA 5.71E-07 mr1830 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
vg0614462540 NA 1.60E-19 mr1846 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
vg0614462540 NA 9.63E-11 mr1846 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
vg0614462540 NA 2.02E-06 mr1608_2 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
vg0614462540 NA 2.15E-13 mr1830_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
vg0614462540 NA 1.42E-10 mr1830_2 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
vg0614462540 NA 8.55E-31 mr1846_2 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
vg0614462540 NA 5.67E-20 mr1846_2 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