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Detailed information for vg0301337606:

Variant ID: vg0301337606 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1337606
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGATTTTGTTTTCGAAGAAAGCTTGATAAAAATCTGATTAGCTTCCACCCACCCCTCGATTTAGAATTAAATTGGGTTTGATCCCTCATGGGGATGTT[C/A]
TCTCATTATTTGCATATAATATATCACTCCACAAACATGCAAGTTCATATTCAACTTCTATATCTTGTAAAAAAACCAAATTTGATTATGAATATACGTT

Reverse complement sequence

AACGTATATTCATAATCAAATTTGGTTTTTTTACAAGATATAGAAGTTGAATATGAACTTGCATGTTTGTGGAGTGATATATTATATGCAAATAATGAGA[G/T]
AACATCCCCATGAGGGATCAAACCCAATTTAATTCTAAATCGAGGGGTGGGTGGAAGCTAATCAGATTTTTATCAAGCTTTCTTCGAAAACAAAATCATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 1.70% 0.76% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.60% 5.20% 2.25% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 87.70% 8.50% 3.78% 0.00% NA
Tropical Japonica  504 98.00% 1.40% 0.60% 0.00% NA
Japonica Intermediate  241 96.70% 2.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0301337606 C -> A LOC_Os03g03164.2 upstream_gene_variant ; 2446.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301337606 C -> A LOC_Os03g03164.1 upstream_gene_variant ; 2461.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301337606 C -> A LOC_Os03g03164.3 upstream_gene_variant ; 2461.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301337606 C -> A LOC_Os03g03150-LOC_Os03g03164 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301337606 NA 5.70E-07 mr1354 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
vg0301337606 9.40E-08 NA mr1310_2 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
vg0301337606 NA 3.29E-06 mr1354_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
vg0301337606 8.38E-06 NA mr1900_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
vg0301337606 NA 1.47E-06 mr1902_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
vg0301337606 1.46E-06 NA mr1959_2 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