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Detailed information for vg1202580538:

Variant ID: vg1202580538 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2580538
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAACACCACCTAGATAGGAGAAGAGCCCCCGGTGAGTGTAACAGCATCTCCAACAGCCTCTCCAAATCGAACTCTCCAAACACCCATAAGCCAACTCTCC[G/A]
TCTGATTTAGCTAGTCAAACTAGATACTCACTCCAACAGACTCTCTATTAATCCTCTCCAAAATAAAATCGGACTCACATGTCAACATCTATCCCCTCTT

Reverse complement sequence

AAGAGGGGATAGATGTTGACATGTGAGTCCGATTTTATTTTGGAGAGGATTAATAGAGAGTCTGTTGGAGTGAGTATCTAGTTTGACTAGCTAAATCAGA[C/T]
GGAGAGTTGGCTTATGGGTGTTTGGAGAGTTCGATTTGGAGAGGCTGTTGGAGATGCTGTTACACTCACCGGGGGCTCTTCTCCTATCTAGGTGGTGTTT

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 86.90% 13.10% 0.00% 0.00% NA
All Indica  2759 85.70% 14.30% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 22.30% 77.70% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 86.50% 13.50% 0.00% 0.00% NA
Indica III  913 83.90% 16.10% 0.00% 0.00% NA
Indica Intermediate  786 79.90% 20.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg1202580538 G -> A LOC_Os12g05609.1 upstream_gene_variant ; 4954.0bp to feature; MODIFIER silent_mutation Average:62.791; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg1202580538 G -> A LOC_Os12g05620.1 downstream_gene_variant ; 3356.0bp to feature; MODIFIER silent_mutation Average:62.791; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg1202580538 G -> A LOC_Os12g05609-LOC_Os12g05620 intergenic_region ; MODIFIER silent_mutation Average:62.791; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202580538 1.80E-06 1.21E-07 mr1071 Ind_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
vg1202580538 NA 5.36E-06 mr1080 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
vg1202580538 NA 4.19E-06 mr1125 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
vg1202580538 NA 8.27E-06 mr1153 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
vg1202580538 NA 7.07E-07 mr1286 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
vg1202580538 NA 3.65E-06 mr1393 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
vg1202580538 NA 8.33E-06 mr1400 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
vg1202580538 NA 2.16E-06 mr1438 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
vg1202580538 NA 4.42E-06 mr1523 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
vg1202580538 NA 7.97E-07 mr1574 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
vg1202580538 NA 1.46E-06 mr1665 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
vg1202580538 NA 4.71E-06 mr1774 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
vg1202580538 NA 3.24E-06 mr1777 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
vg1202580538 NA 5.94E-06 mr1795 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