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Detailed information for vg1222068437:

Variant ID: vg1222068437 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22068437
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCACCACATGCGATGGCATGCATAGCGAGTTTAGTACCACCTTACTTATTCTAGGAGAGAGGGATCTCCTTAGGGAGGATGCCCTCCTAGCCACTTGAAG[T/C]
ATGTGAGATGGAGAGAAGAGGGGGAACACACGCGCTTGCTCGCTTGCCGGGCCGGGCAGGCGGCGCGCGACGTACGCATCGAATAGATGCAGCCTGCTTT

Reverse complement sequence

AAAGCAGGCTGCATCTATTCGATGCGTACGTCGCGCGCCGCCTGCCCGGCCCGGCAAGCGAGCAAGCGCGTGTGTTCCCCCTCTTCTCTCCATCTCACAT[A/G]
CTTCAAGTGGCTAGGAGGGCATCCTCCCTAAGGAGATCCCTCTCTCCTAGAATAAGTAAGGTGGTACTAAACTCGCTATGCATGCCATCGCATGTGGTGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.60% 6.80% 1.65% 0.00% NA
All Indica  2759 92.30% 6.90% 0.83% 0.00% NA
All Japonica  1512 99.70% 0.10% 0.13% 0.00% NA
Aus  269 36.10% 45.40% 18.59% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 92.50% 6.00% 1.51% 0.00% NA
Indica III  913 87.60% 11.30% 1.10% 0.00% NA
Indica Intermediate  786 93.40% 5.90% 0.76% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 94.80% 2.10% 3.12% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1222068437 T -> C LOC_Os12g36030-LOC_Os12g36040 intergenic_region ; MODIFIER silent_mutation Average:42.765; most accessible tissue: Callus, score: 66.764 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222068437 3.97E-06 NA mr1190 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
vg1222068437 NA 4.55E-07 mr1343 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
vg1222068437 NA 9.68E-07 mr1654 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
vg1222068437 NA 2.33E-18 mr1855 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
vg1222068437 NA 2.61E-06 mr1608_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
vg1222068437 NA 6.64E-10 mr1818_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
vg1222068437 NA 2.32E-10 mr1897_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