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Detailed information for vg1219437084:

Variant ID: vg1219437084 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19437084
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTTCCCACGGAGCACCTCGCCGCCGCCTCAAACGGATCAGCCGCCGCCACACCGCCTCCTCCCACGAAGCAAGTCGCCGCCGACAAAGCAACTCGCCGC[C/T]
AACAAAGCACGAAGCAACTCGCCGCCGCCTCCCACGGATCGGATCAGAAAGGAATGGCTGAGATTTGGTAGAAAACCCTATTTCCCTCCCCGGACACTCA

Reverse complement sequence

TGAGTGTCCGGGGAGGGAAATAGGGTTTTCTACCAAATCTCAGCCATTCCTTTCTGATCCGATCCGTGGGAGGCGGCGGCGAGTTGCTTCGTGCTTTGTT[G/A]
GCGGCGAGTTGCTTTGTCGGCGGCGACTTGCTTCGTGGGAGGAGGCGGTGTGGCGGCGGCTGATCCGTTTGAGGCGGCGGCGAGGTGCTCCGTGGGAAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 5.60% 0.04% 0.00% NA
All Indica  2759 90.40% 9.50% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 80.00% 19.70% 0.34% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 91.50% 8.50% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 95.60% 4.40% 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
vg1219437084 C -> T LOC_Os12g32210.1 upstream_gene_variant ; 4092.0bp to feature; MODIFIER silent_mutation Average:54.258; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg1219437084 C -> T LOC_Os12g32210.2 upstream_gene_variant ; 3634.0bp to feature; MODIFIER silent_mutation Average:54.258; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg1219437084 C -> T LOC_Os12g32200.1 intron_variant ; MODIFIER silent_mutation Average:54.258; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219437084 3.15E-06 NA mr1111 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
vg1219437084 NA 2.37E-06 mr1111 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
vg1219437084 8.80E-06 NA mr1588 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
vg1219437084 NA 2.24E-06 mr1588 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