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Detailed information for vg0108352749:

Variant ID: vg0108352749 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8352749
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAATTGGCTCCAGGCAGGGTTTACCGCGGGGAACAGTAATATAAATACAATAGTAACCTTCTTAAATTTAAATAAATTTAAAAAATAATTTAAATTTTT[G/A]
ATAAATTTTGTACGATTTTTTACGGTTACCACGGTTACCGCGCGGTAACCGTGCTTACCACCGGGACGCGGTTTGGAAAACCCTGGCTTGGTAAGCTTTT

Reverse complement sequence

AAAAGCTTACCAAGCCAGGGTTTTCCAAACCGCGTCCCGGTGGTAAGCACGGTTACCGCGCGGTAACCGTGGTAACCGTAAAAAATCGTACAAAATTTAT[C/T]
AAAAATTTAAATTATTTTTTAAATTTATTTAAATTTAAGAAGGTTACTATTGTATTTATATTACTGTTCCCCGCGGTAAACCCTGCCTGGAGCCAATTGC

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 99.00% 0.90% 0.13% 0.00% NA
All Indica  2759 99.40% 0.50% 0.11% 0.00% NA
All Japonica  1512 98.40% 1.60% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.20% 0.50% 0.22% 0.00% NA
Indica Intermediate  786 99.00% 0.90% 0.13% 0.00% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 1.00% 3.12% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0108352749 G -> A LOC_Os01g14910.1 upstream_gene_variant ; 1707.0bp to feature; MODIFIER N Average:65.146; most accessible tissue: Callus, score: 80.844 N N N N
vg0108352749 G -> A LOC_Os01g14900.1 downstream_gene_variant ; 1743.0bp to feature; MODIFIER N Average:65.146; most accessible tissue: Callus, score: 80.844 N N N N
vg0108352749 G -> A LOC_Os01g14900-LOC_Os01g14910 intergenic_region ; MODIFIER N Average:65.146; most accessible tissue: Callus, score: 80.844 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0108352749 NA 6.59E-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
vg0108352749 NA 8.67E-06 mr1829 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
vg0108352749 NA 3.07E-07 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
vg0108352749 NA 2.46E-11 mr1829_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
vg0108352749 NA 2.39E-09 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