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Detailed information for vg1203926835:

Variant ID: vg1203926835 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3926835
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTTCTGAGTTGTGTATGTCCAGATTCAAACCCAGAAGTGGGTTTTTTTAGGGAGTACGTGCTACTAACACCATGAACTCACGTTTCAACATATAATTTC[G/A]
TTTGGCTATTTAGGCTTAAGTGATTTATGTGATCAAGATGACGTGGGTGATGCAATAACTAGCAATATGAGCAAACATCATGATTTTTTATGCCCAAACT

Reverse complement sequence

AGTTTGGGCATAAAAAATCATGATGTTTGCTCATATTGCTAGTTATTGCATCACCCACGTCATCTTGATCACATAAATCACTTAAGCCTAAATAGCCAAA[C/T]
GAAATTATATGTTGAAACGTGAGTTCATGGTGTTAGTAGCACGTACTCCCTAAAAAAACCCACTTCTGGGTTTGAATCTGGACATACACAACTCAGAAGT

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 95.30% 4.30% 0.38% 0.00% NA
All Indica  2759 99.80% 0.20% 0.04% 0.00% NA
All Japonica  1512 86.40% 12.60% 1.06% 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 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 2.60% 0.78% 0.00% NA
Tropical Japonica  504 70.20% 29.20% 0.60% 0.00% NA
Japonica Intermediate  241 87.60% 9.50% 2.90% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 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
vg1203926835 G -> A LOC_Os12g07770-LOC_Os12g07780 intergenic_region ; MODIFIER silent_mutation Average:36.235; most accessible tissue: Zhenshan97 flower, score: 58.632 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203926835 NA 3.97E-08 mr1013 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
vg1203926835 NA 1.29E-06 mr1031 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
vg1203926835 NA 1.16E-07 mr1034 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
vg1203926835 NA 3.69E-07 mr1056 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