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Detailed information for vg1218120371:

Variant ID: vg1218120371 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18120371
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGCCTGAGAGGTGGCCAGACGCAGAGGTCATCGCTCAGGCTCTACGGCGAGATCACCGTCTCCACCGGCAAGGTCAGCGTCGACGTCGTCCCTGCAGC[G/A]
GCGCGCGGAATGGCCGCCGGCGTGGCCTATCCTGTGGCCAGGGGAGACGGCTGGATGGAGCTCAAGCTGGCCGAGTTTGCTGCCGACGAGAAGCTGCTCG

Reverse complement sequence

CGAGCAGCTTCTCGTCGGCAGCAAACTCGGCCAGCTTGAGCTCCATCCAGCCGTCTCCCCTGGCCACAGGATAGGCCACGCCGGCGGCCATTCCGCGCGC[C/T]
GCTGCAGGGACGACGTCGACGCTGACCTTGCCGGTGGAGACGGTGATCTCGCCGTAGAGCCTGAGCGATGACCTCTGCGTCTGGCCACCTCTCAGGCCGA

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 95.60% 4.30% 0.11% 0.00% NA
All Indica  2759 92.60% 7.20% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.90% 5.50% 0.50% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 91.80% 8.10% 0.11% 0.00% NA
Indica Intermediate  786 89.40% 10.40% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1218120371 G -> A LOC_Os12g30180.1 synonymous_variant ; p.Ala413Ala; LOW synonymous_codon Average:76.064; most accessible tissue: Zhenshan97 young leaf, score: 87.723 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218120371 3.20E-08 3.20E-08 mr1321 Ind_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
vg1218120371 4.63E-06 2.87E-06 mr1322 Ind_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
vg1218120371 3.44E-08 3.44E-08 mr1323 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
vg1218120371 2.35E-07 6.91E-08 mr1324 Ind_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
vg1218120371 3.82E-07 6.91E-08 mr1325 Ind_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
vg1218120371 1.13E-06 1.99E-07 mr1326 Ind_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
vg1218120371 7.30E-07 3.68E-07 mr1335 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
vg1218120371 6.08E-06 4.69E-08 mr1336 Ind_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
vg1218120371 3.33E-06 3.33E-06 mr1527 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
vg1218120371 NA 2.69E-06 mr1553 Ind_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
vg1218120371 5.92E-06 4.66E-06 mr1712 Ind_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
vg1218120371 NA 2.99E-06 mr1732 Ind_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