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Detailed information for vg1200363040:

Variant ID: vg1200363040 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 363040
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCGGTAACTGCCGATGCACACTATAGCCGATGCGGTTTCGAAGCCGATTCGTACCCTGTTTCCGTTATTGATTTCCTTGCAAATCCGCTTCGGCGTTAA[C/T]
TCCAAATCTGATGGATGATTTACCAAATTTCGTTGTTAACACCGGGGTAGTGCGCCTGCGCACTGCTACATGTTAGGCGACATGCCGCCTGACATCCCCT

Reverse complement sequence

AGGGGATGTCAGGCGGCATGTCGCCTAACATGTAGCAGTGCGCAGGCGCACTACCCCGGTGTTAACAACGAAATTTGGTAAATCATCCATCAGATTTGGA[G/A]
TTAACGCCGAAGCGGATTTGCAAGGAAATCAATAACGGAAACAGGGTACGAATCGGCTTCGAAACCGCATCGGCTATAGTGTGCATCGGCAGTTACCGAA

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 97.70% 1.90% 0.34% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 93.10% 6.00% 0.93% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 97.50% 1.40% 1.04% 0.00% NA
Tropical Japonica  504 97.00% 2.80% 0.20% 0.00% NA
Japonica Intermediate  241 71.00% 27.00% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1200363040 C -> T LOC_Os12g01590.1 upstream_gene_variant ; 3679.0bp to feature; MODIFIER silent_mutation Average:59.584; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg1200363040 C -> T LOC_Os12g01610.1 upstream_gene_variant ; 3317.0bp to feature; MODIFIER silent_mutation Average:59.584; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg1200363040 C -> T LOC_Os12g01600.1 downstream_gene_variant ; 1199.0bp to feature; MODIFIER silent_mutation Average:59.584; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg1200363040 C -> T LOC_Os12g01590-LOC_Os12g01600 intergenic_region ; MODIFIER silent_mutation Average:59.584; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200363040 NA 7.65E-06 mr1117 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
vg1200363040 3.84E-06 4.81E-08 mr1691 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
vg1200363040 NA 6.50E-08 mr1693 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
vg1200363040 NA 9.08E-06 mr1720 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
vg1200363040 NA 2.72E-06 mr1117_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
vg1200363040 NA 1.15E-06 mr1496_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