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Detailed information for vg0128647202:

Variant ID: vg0128647202 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28647202
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTACCTCTCTGTCATTTATTGGACAGATGGATGTGGAGCAACATGGTGATGGAGAGATGGCCGAAGAGGAAGAGGTTTTTGATGAAGGAAGCACATC[G/A]
TCAAGTGATGATGAGATTATTTCCATGTGCCGCAAGAATATGAACATGGCTCAAACTATGGTTGCTCAACTTGTCCCTATCCTTGGTATGTACTCCGAGC

Reverse complement sequence

GCTCGGAGTACATACCAAGGATAGGGACAAGTTGAGCAACCATAGTTTGAGCCATGTTCATATTCTTGCGGCACATGGAAATAATCTCATCATCACTTGA[C/T]
GATGTGCTTCCTTCATCAAAAACCTCTTCCTCTTCGGCCATCTCTCCATCACCATGTTGCTCCACATCCATCTGTCCAATAAATGACAGAGAGGTAATAT

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 77.60% 3.80% 3.64% 15.00% NA
All Indica  2759 76.40% 0.90% 4.86% 17.83% NA
All Japonica  1512 90.40% 0.00% 0.79% 8.80% NA
Aus  269 32.70% 41.30% 4.46% 21.56% NA
Indica I  595 89.10% 0.00% 3.70% 7.23% NA
Indica II  465 55.50% 0.60% 12.04% 31.83% NA
Indica III  913 76.70% 0.50% 1.64% 21.14% NA
Indica Intermediate  786 78.80% 2.30% 5.22% 13.74% NA
Temperate Japonica  767 99.60% 0.00% 0.13% 0.26% NA
Tropical Japonica  504 74.00% 0.00% 1.59% 24.40% NA
Japonica Intermediate  241 95.40% 0.00% 1.24% 3.32% NA
VI/Aromatic  96 26.00% 37.50% 12.50% 23.96% NA
Intermediate  90 87.80% 6.70% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0128647202 G -> A LOC_Os01g49870.1 synonymous_variant ; p.Ser234Ser; LOW synonymous_codon Average:30.663; most accessible tissue: Callus, score: 62.675 N N N N
vg0128647202 G -> DEL LOC_Os01g49870.1 N frameshift_variant Average:30.663; most accessible tissue: Callus, score: 62.675 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128647202 NA 7.25E-13 mr1612 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
vg0128647202 NA 1.99E-06 mr1652 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
vg0128647202 NA 1.55E-08 mr1989 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
vg0128647202 NA 9.92E-08 mr1126_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
vg0128647202 NA 5.44E-10 mr1166_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
vg0128647202 NA 1.81E-07 mr1567_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
vg0128647202 3.56E-06 NA mr1593_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
vg0128647202 NA 6.87E-13 mr1612_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
vg0128647202 NA 1.62E-07 mr1765_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