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Detailed information for vg0112881406:

Variant ID: vg0112881406 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 12881406
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTGAGGGTAGGTAAAATGGTAGAAGTTGGTTTTTTTGGAACAAAATTCAAATTCTAGAAGTTGAGTTTTTTTGGGACGGAGGGAGTATGTCCAAAGTC[G/A]
TAGTAGGATGTGTCACATTTAGTATTAGATTGGTTTTCTACGGGACAAAGGGAGTAACCAACATATTTAACAAATATTATAATTTTAATATTTAATAATA

Reverse complement sequence

TATTATTAAATATTAAAATTATAATATTTGTTAAATATGTTGGTTACTCCCTTTGTCCCGTAGAAAACCAATCTAATACTAAATGTGACACATCCTACTA[C/T]
GACTTTGGACATACTCCCTCCGTCCCAAAAAAACTCAACTTCTAGAATTTGAATTTTGTTCCAAAAAAACCAACTTCTACCATTTTACCTACCCTCAACA

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 85.00% 14.80% 0.15% 0.00% NA
All Indica  2759 88.90% 11.10% 0.00% 0.00% NA
All Japonica  1512 91.30% 8.30% 0.40% 0.00% NA
Aus  269 6.70% 93.30% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 83.50% 16.50% 0.00% 0.00% NA
Indica Intermediate  786 84.70% 15.30% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 77.20% 21.80% 0.99% 0.00% NA
Japonica Intermediate  241 94.20% 5.40% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 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
vg0112881406 G -> A LOC_Os01g22920.1 downstream_gene_variant ; 3068.0bp to feature; MODIFIER silent_mutation Average:32.507; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0112881406 G -> A LOC_Os01g22910.1 intron_variant ; MODIFIER silent_mutation Average:32.507; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0112881406 NA 8.98E-08 mr1530 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
vg0112881406 NA 1.48E-11 mr1696 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
vg0112881406 NA 4.41E-10 mr1047_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
vg0112881406 2.96E-06 NA mr1134_2 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
vg0112881406 NA 2.33E-06 mr1456_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
vg0112881406 NA 5.07E-17 mr1530_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
vg0112881406 NA 6.37E-07 mr1792_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
vg0112881406 NA 6.57E-13 mr1803_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
vg0112881406 NA 2.60E-08 mr1808_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
vg0112881406 NA 9.82E-07 mr1815_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
vg0112881406 NA 3.47E-06 mr1850_2 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