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Detailed information for vg1203473350:

Variant ID: vg1203473350 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3473350
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGTTACTCCCTTCGTTTCAGGTTATAAGATGTTTTGACTTTGGTCAAAGTTAAACTGCTTTAGGTTTGACCAAGTTTATAGAAAAAATAATAATATTTT[C/T]
GACCCAAGATAAATTTATTATAAAAATGTATTTAATTGTTAATTTAATAAAATGAATGTAAATATTACTATATTTCTCTATAAACATAGTCAAACTTGAA

Reverse complement sequence

TTCAAGTTTGACTATGTTTATAGAGAAATATAGTAATATTTACATTCATTTTATTAAATTAACAATTAAATACATTTTTATAATAAATTTATCTTGGGTC[G/A]
AAAATATTATTATTTTTTCTATAAACTTGGTCAAACCTAAAGCAGTTTAACTTTGACCAAAGTCAAAACATCTTATAACCTGAAACGAAGGGAGTAACTC

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 94.10% 3.80% 2.07% 0.00% NA
All Indica  2759 99.70% 0.00% 0.22% 0.00% NA
All Japonica  1512 82.40% 11.70% 5.89% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.20% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 70.40% 19.20% 10.43% 0.00% NA
Tropical Japonica  504 99.00% 0.40% 0.60% 0.00% NA
Japonica Intermediate  241 85.90% 11.60% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 1.10% 3.33% 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
vg1203473350 C -> T LOC_Os12g07080.1 downstream_gene_variant ; 1153.0bp to feature; MODIFIER silent_mutation Average:25.469; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg1203473350 C -> T LOC_Os12g07080-LOC_Os12g07100 intergenic_region ; MODIFIER silent_mutation Average:25.469; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203473350 1.84E-06 NA mr1074_2 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
vg1203473350 3.91E-06 NA mr1081_2 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
vg1203473350 NA 1.20E-06 mr1221_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
vg1203473350 NA 6.26E-07 mr1358_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
vg1203473350 3.51E-06 3.51E-06 mr1474_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
vg1203473350 9.85E-06 9.85E-06 mr1571_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
vg1203473350 8.13E-06 NA mr1748_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