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Detailed information for vg0106723726:

Variant ID: vg0106723726 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6723726
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACGACACCTTTGACTTTGTGAGGAAAATATCGTCGTTGCCTAGCTTGCTGCCTCCAACGACACAACAGCTCCGACTTCATAAGAAGCGTCGTCATTTC[C/G]
AAGCCCGTTGCAAGGGATAAAGCAGCTTCAATATCTCATGGTGGACATCAGCCAAAGACATCGAGAAAACCACTTCAAACACATGACAGGCACCAACACA

Reverse complement sequence

TGTGTTGGTGCCTGTCATGTGTTTGAAGTGGTTTTCTCGATGTCTTTGGCTGATGTCCACCATGAGATATTGAAGCTGCTTTATCCCTTGCAACGGGCTT[G/C]
GAAATGACGACGCTTCTTATGAAGTCGGAGCTGTTGTGTCGTTGGAGGCAGCAAGCTAGGCAACGACGATATTTTCCTCACAAAGTCAAAGGTGTCGTGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.90% 5.50% 0.61% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 82.00% 16.20% 1.79% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 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 84.40% 13.40% 2.22% 0.00% NA
Tropical Japonica  504 77.40% 21.80% 0.79% 0.00% NA
Japonica Intermediate  241 84.20% 13.30% 2.49% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 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
vg0106723726 C -> G LOC_Os01g12304.1 upstream_gene_variant ; 3778.0bp to feature; MODIFIER silent_mutation Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0106723726 C -> G LOC_Os01g12310.1 downstream_gene_variant ; 1126.0bp to feature; MODIFIER silent_mutation Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0106723726 C -> G LOC_Os01g12320.1 downstream_gene_variant ; 1213.0bp to feature; MODIFIER silent_mutation Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0106723726 C -> G LOC_Os01g12320.3 downstream_gene_variant ; 1213.0bp to feature; MODIFIER silent_mutation Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0106723726 C -> G LOC_Os01g12320.2 downstream_gene_variant ; 1213.0bp to feature; MODIFIER silent_mutation Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N
vg0106723726 C -> G LOC_Os01g12310-LOC_Os01g12320 intergenic_region ; MODIFIER silent_mutation Average:61.623; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106723726 2.29E-06 2.85E-06 mr1219 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