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Detailed information for vg1218416620:

Variant ID: vg1218416620 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18416620
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


AGGGTCGTGAAGGAGAAGGTTGCCAGGTGGAAGGAAAGCGACGCCGGACTAGACATGGCCGCCGAGGAAGGAGCAGAGCCTTCGGCGCCCACTGCCGAAG[A/T]
TGGAGGAGGACAAGCGACATCACAACTGCCTTCGGCCCCTGCAACCTCCGTGCAAGTGCCGAACGCGGCCGACGTGGCGAAGGCGGCTGCGGCGGCAAGG

Reverse complement sequence

CCTTGCCGCCGCAGCCGCCTTCGCCACGTCGGCCGCGTTCGGCACTTGCACGGAGGTTGCAGGGGCCGAAGGCAGTTGTGATGTCGCTTGTCCTCCTCCA[T/A]
CTTCGGCAGTGGGCGCCGAAGGCTCTGCTCCTTCCTCGGCGGCCATGTCTAGTCCGGCGTCGCTTTCCTTCCACCTGGCAACCTTCTCCTTCACGACCCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.90% 20.60% 1.44% 29.07% NA
All Indica  2759 23.10% 34.90% 2.36% 39.65% NA
All Japonica  1512 98.20% 0.10% 0.00% 1.72% NA
Aus  269 14.10% 0.70% 1.12% 84.01% NA
Indica I  595 38.50% 20.30% 0.67% 40.50% NA
Indica II  465 28.20% 20.90% 2.80% 48.17% NA
Indica III  913 9.50% 53.60% 2.41% 34.50% NA
Indica Intermediate  786 24.20% 32.60% 3.31% 39.95% NA
Temperate Japonica  767 98.80% 0.00% 0.00% 1.17% NA
Tropical Japonica  504 99.00% 0.20% 0.00% 0.79% NA
Japonica Intermediate  241 94.60% 0.00% 0.00% 5.39% NA
VI/Aromatic  96 82.30% 1.00% 0.00% 16.67% NA
Intermediate  90 77.80% 8.90% 0.00% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218416620 A -> DEL LOC_Os12g30660.1 N frameshift_variant Average:42.665; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg1218416620 A -> T LOC_Os12g30660.1 missense_variant ; p.Asp16Val; MODERATE nonsynonymous_codon ; D16V Average:42.665; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 possibly damaging 1.86 TOLERATED 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218416620 NA 8.99E-06 mr1066 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
vg1218416620 NA 3.07E-11 mr1425 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
vg1218416620 NA 2.65E-09 mr1425 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
vg1218416620 NA 1.29E-06 mr1851 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
vg1218416620 NA 6.69E-08 mr1321_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
vg1218416620 NA 4.05E-08 mr1539_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
vg1218416620 1.14E-06 NA mr1540_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
vg1218416620 1.57E-06 8.41E-12 mr1540_2 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
vg1218416620 4.37E-06 NA mr1732_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
vg1218416620 4.64E-06 1.07E-10 mr1732_2 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
vg1218416620 NA 2.17E-06 mr1864_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
vg1218416620 NA 2.50E-06 mr1910_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