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Detailed information for vg1212504438:

Variant ID: vg1212504438 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12504438
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTATGCTTTTAGATTCACGTTGTTCATCAAAAAGGCATGGGGGCATGTGTTTACACCCAAATTTGGCACCTAGGGTTAAAATAGGAAAGATTCCCAAAA[G/A]
TTGGAAGTCTACCGATTTCCTCCGAGTGGGCCGGTCTGACTGCCGTGTGTTGGGCGGTCAGACCGTCGGTTGAGGGCCGGTCAGACCGGCCAGTTTGACT

Reverse complement sequence

AGTCAAACTGGCCGGTCTGACCGGCCCTCAACCGACGGTCTGACCGCCCAACACACGGCAGTCAGACCGGCCCACTCGGAGGAAATCGGTAGACTTCCAA[C/T]
TTTTGGGAATCTTTCCTATTTTAACCCTAGGTGCCAAATTTGGGTGTAAACACATGCCCCCATGCCTTTTTGATGAACAACGTGAATCTAAAAGCATAGA

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 95.80% 2.90% 1.25% 0.00% NA
All Indica  2759 99.90% 0.10% 0.07% 0.00% NA
All Japonica  1512 87.70% 8.80% 3.51% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 98.40% 0.10% 1.43% 0.00% NA
Tropical Japonica  504 67.90% 25.40% 6.75% 0.00% NA
Japonica Intermediate  241 95.00% 1.70% 3.32% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 93.30% 4.40% 2.22% 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
vg1212504438 G -> A LOC_Os12g22190.1 downstream_gene_variant ; 322.0bp to feature; MODIFIER silent_mutation Average:49.898; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg1212504438 G -> A LOC_Os12g22190-LOC_Os12g22200 intergenic_region ; MODIFIER silent_mutation Average:49.898; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1212504438 NA 7.86E-06 mr1448 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
vg1212504438 4.76E-06 3.63E-09 mr1471 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
vg1212504438 NA 2.92E-06 mr1642 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
vg1212504438 NA 8.70E-07 mr1696 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
vg1212504438 NA 7.85E-07 mr1653_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