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Detailed information for vg1226169508:

Variant ID: vg1226169508 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 26169508
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCATTTAAAATTTATTTGTAAATATAAGAAATTTTAGAGTACTAGTAATTCCCATATTAATTACCTCATATTAATCATATTGATTTTTCTATCCTATC[C/A]
TCAACTATCAGGGCATAAACCATACCTCATTTACCTCATTTAATGAGGAACACCGGAATCTTTTCTTCCTAACCTTAATATCTACTATAAATAACTAAAT

Reverse complement sequence

ATTTAGTTATTTATAGTAGATATTAAGGTTAGGAAGAAAAGATTCCGGTGTTCCTCATTAAATGAGGTAAATGAGGTATGGTTTATGCCCTGATAGTTGA[G/T]
GATAGGATAGAAAAATCAATATGATTAATATGAGGTAATTAATATGGGAATTACTAGTACTCTAAAATTTCTTATATTTACAAATAAATTTTAAATGGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 1.10% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 97.30% 2.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 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 94.80% 5.20% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1226169508 C -> A LOC_Os12g42200.1 upstream_gene_variant ; 3363.0bp to feature; MODIFIER silent_mutation Average:40.888; most accessible tissue: Minghui63 root, score: 71.259 N N N N
vg1226169508 C -> A LOC_Os12g42190-LOC_Os12g42200 intergenic_region ; MODIFIER silent_mutation Average:40.888; most accessible tissue: Minghui63 root, score: 71.259 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1226169508 NA 9.05E-06 mr1069 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
vg1226169508 3.69E-06 NA mr1124 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
vg1226169508 2.47E-06 2.47E-06 mr1200 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
vg1226169508 7.45E-06 9.65E-06 mr1441 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
vg1226169508 1.10E-06 1.10E-06 mr1861 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