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Detailed information for vg0132643720:

Variant ID: vg0132643720 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 32643720
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: 300. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGTAGTTCTATAATTTTGTAGTAACAAAACATGATAGTTGAGGAAGGCTCAGGCATCTTCCTTTAATTTCGAGCCTCATTCTTAATAATATCTGATAT[G/A]
AGAGCCCCTCCTCTCATATCCAGCGTTTTAATTTTTTAGTTTTAGGACCAGTGAGCAAGAATGTATAATTATTCATACATGGAAGGAGTGTAGCTGTATT

Reverse complement sequence

AATACAGCTACACTCCTTCCATGTATGAATAATTATACATTCTTGCTCACTGGTCCTAAAACTAAAAAATTAAAACGCTGGATATGAGAGGAGGGGCTCT[C/T]
ATATCAGATATTATTAAGAATGAGGCTCGAAATTAAAGGAAGATGCCTGAGCCTTCCTCAACTATCATGTTTTGTTACTACAAAATTATAGAACTACAAA

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 96.20% 2.70% 1.14% 0.00% NA
All Indica  2759 93.50% 4.60% 1.96% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.20% 11.80% 6.05% 0.00% NA
Indica II  465 96.80% 2.80% 0.43% 0.00% NA
Indica III  913 99.30% 0.50% 0.11% 0.00% NA
Indica Intermediate  786 93.30% 4.80% 1.91% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0132643720 G -> A LOC_Os01g56590.1 intron_variant ; MODIFIER silent_mutation Average:44.897; most accessible tissue: Callus, score: 87.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0132643720 NA 2.65E-10 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0132643720 6.99E-06 1.11E-08 mr1008 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
vg0132643720 4.44E-06 6.45E-09 mr1009 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
vg0132643720 7.10E-06 1.95E-07 mr1014 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
vg0132643720 9.32E-06 5.16E-08 mr1015 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
vg0132643720 1.89E-08 1.67E-11 mr1008_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
vg0132643720 NA 7.40E-07 mr1015_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