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Detailed information for vg1202269648:

Variant ID: vg1202269648 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2269648
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGTTGTTTCCATATAGGACATGGTATGTGGTGGGTCCTGCCGAGATTTAGTCAACTACTATTAGGTATGTGGTATACATAACCCTGACAGTAGCCCCC[G/T]
ACTTCGATGCAAATGAATGAATTCATATTCTCAACTGCGCAGACATTGGAGTAACTATTATCGAGCTCATGTGACAGTTCTCGGTGAGTTTAGAGAGAAC

Reverse complement sequence

GTTCTCTCTAAACTCACCGAGAACTGTCACATGAGCTCGATAATAGTTACTCCAATGTCTGCGCAGTTGAGAATATGAATTCATTCATTTGCATCGAAGT[C/A]
GGGGGCTACTGTCAGGGTTATGTATACCACATACCTAATAGTAGTTGACTAAATCTCGGCAGGACCCACCACATACCATGTCCTATATGGAAACAACCTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 1.50% 1.27% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.50% 4.60% 3.90% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 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 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 84.50% 8.90% 6.65% 0.00% NA
Tropical Japonica  504 99.00% 0.00% 0.99% 0.00% NA
Japonica Intermediate  241 98.30% 0.40% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg1202269648 G -> T LOC_Os12g05130.1 downstream_gene_variant ; 4312.0bp to feature; MODIFIER silent_mutation Average:45.168; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg1202269648 G -> T LOC_Os12g05144.1 downstream_gene_variant ; 2545.0bp to feature; MODIFIER silent_mutation Average:45.168; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg1202269648 G -> T LOC_Os12g05151.1 downstream_gene_variant ; 3983.0bp to feature; MODIFIER silent_mutation Average:45.168; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg1202269648 G -> T LOC_Os12g05130-LOC_Os12g05144 intergenic_region ; MODIFIER silent_mutation Average:45.168; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202269648 2.82E-06 3.44E-08 mr1210 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
vg1202269648 6.48E-06 2.87E-08 mr1305 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
vg1202269648 1.20E-07 8.57E-11 mr1585 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
vg1202269648 7.13E-07 6.45E-09 mr1586 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
vg1202269648 NA 8.19E-07 mr1765 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
vg1202269648 NA 1.37E-06 mr1585_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