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Detailed information for vg0121863168:

Variant ID: vg0121863168 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 21863168
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTAGCAATTGATTTGTTCCTGGCCCTGGCCTACCTCCATTGTGAATTGAACTTGAGGACTCACCCGTCAATTTGAAAATTTTCCTGCAGGGGTTAGTC[C/G]
ACATAAGATATATATCCAATGTCTATGAACATATTAACTCTGAAATTCATTAATCAAACTAAACTCCATGTCCAATTTGATTAAAATAGACTATTTTAAC

Reverse complement sequence

GTTAAAATAGTCTATTTTAATCAAATTGGACATGGAGTTTAGTTTGATTAATGAATTTCAGAGTTAATATGTTCATAGACATTGGATATATATCTTATGT[G/C]
GACTAACCCCTGCAGGAAAATTTTCAAATTGACGGGTGAGTCCTCAAGTTCAATTCACAATGGAGGTAGGCCAGGGCCAGGAACAAATCAATTGCTAACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.50% 5.40% 20.74% 20.44% NA
All Indica  2759 27.60% 9.00% 31.06% 32.40% NA
All Japonica  1512 97.60% 0.00% 0.86% 1.52% NA
Aus  269 58.00% 0.40% 29.37% 12.27% NA
Indica I  595 8.90% 3.50% 22.52% 65.04% NA
Indica II  465 29.70% 10.30% 27.31% 32.69% NA
Indica III  913 29.60% 12.40% 40.53% 17.52% NA
Indica Intermediate  786 38.20% 8.30% 28.75% 24.81% NA
Temperate Japonica  767 98.30% 0.00% 0.78% 0.91% NA
Tropical Japonica  504 98.20% 0.00% 0.20% 1.59% NA
Japonica Intermediate  241 94.20% 0.00% 2.49% 3.32% NA
VI/Aromatic  96 70.80% 3.10% 20.83% 5.21% NA
Intermediate  90 73.30% 2.20% 12.22% 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
vg0121863168 C -> G LOC_Os01g38920-LOC_Os01g38930 intergenic_region ; MODIFIER silent_mutation Average:8.01; most accessible tissue: Callus, score: 18.947 N N N N
vg0121863168 C -> DEL N N silent_mutation Average:8.01; most accessible tissue: Callus, score: 18.947 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0121863168 8.85E-06 8.85E-06 mr1027 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
vg0121863168 NA 1.39E-07 mr1053 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
vg0121863168 NA 1.57E-06 mr1709 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
vg0121863168 NA 1.53E-06 mr1027_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
vg0121863168 4.28E-06 4.27E-06 mr1473_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
vg0121863168 7.17E-06 7.17E-06 mr1473_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
vg0121863168 4.36E-06 4.35E-06 mr1630_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
vg0121863168 8.38E-06 8.38E-06 mr1630_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