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Detailed information for vg1203005112:

Variant ID: vg1203005112 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3005112
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


AAGTTTGGTTAAAATTGGAACGATGTGATGGAAACGTTGAAAGTTTATGTGTGTAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAAAAAAAA[T/A]
TTAGAACTAAACAAGGCCTCTATCCGTTCTAACATATAACGGATCCTAAATGAATAGAATATTTTATAGGGTTTGTTGGAACTATGCCACCCTAATTTTA

Reverse complement sequence

TAAAATTAGGGTGGCATAGTTCCAACAAACCCTATAAAATATTCTATTCATTTAGGATCCGTTATATGTTAGAACGGATAGAGGCCTTGTTTAGTTCTAA[A/T]
TTTTTTTTTCAAACTTTCAACTTTTTCATCACATCAAAACTTTCCTACACACATAAACTTTCAACGTTTCCATCACATCGTTCCAATTTTAACCAAACTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.80% 12.90% 0.25% 0.00% NA
All Indica  2759 83.40% 16.20% 0.40% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 45.70% 53.90% 0.37% 0.00% NA
Indica I  595 90.60% 9.10% 0.34% 0.00% NA
Indica II  465 84.30% 15.50% 0.22% 0.00% NA
Indica III  913 80.00% 19.70% 0.33% 0.00% NA
Indica Intermediate  786 81.40% 17.90% 0.64% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1203005112 T -> A LOC_Os12g06290.1 downstream_gene_variant ; 2458.0bp to feature; MODIFIER silent_mutation Average:47.224; most accessible tissue: Minghui63 root, score: 73.351 N N N N
vg1203005112 T -> A LOC_Os12g06280-LOC_Os12g06290 intergenic_region ; MODIFIER silent_mutation Average:47.224; most accessible tissue: Minghui63 root, score: 73.351 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203005112 NA 4.59E-06 mr1048 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
vg1203005112 NA 1.74E-06 mr1196 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
vg1203005112 NA 2.06E-07 mr1207 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
vg1203005112 NA 3.67E-06 mr1286 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
vg1203005112 NA 8.58E-06 mr1287 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
vg1203005112 NA 2.14E-06 mr1353 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
vg1203005112 NA 7.74E-06 mr1374 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
vg1203005112 NA 5.00E-06 mr1472 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
vg1203005112 NA 1.44E-06 mr1485 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
vg1203005112 NA 5.80E-06 mr1516 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
vg1203005112 NA 8.65E-06 mr1569 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
vg1203005112 1.70E-06 1.70E-06 mr1569 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
vg1203005112 NA 5.21E-07 mr1574 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
vg1203005112 NA 4.93E-06 mr1634 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
vg1203005112 NA 2.14E-06 mr1665 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
vg1203005112 NA 3.66E-06 mr1759 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
vg1203005112 NA 4.03E-07 mr1774 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
vg1203005112 NA 8.04E-06 mr1948 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
vg1203005112 NA 8.30E-06 mr1972 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
vg1203005112 NA 5.51E-06 mr1988 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