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Detailed information for vg0324719195:

Variant ID: vg0324719195 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24719195
Reference Allele: AAlternative Allele: T,C
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGTTCGGGTTGCTACAGTGTCTTGAGGGGGGGTATAGGCAATATTTGTGAAATGCTGTAATGCGGAGAGGGCCGAGTGCAAAAGTGTTGCCTACGTGG[A/T,C]
GCGCTAGGTTGGCAGTTAATCGCAGTAGTCAAAGGGCTATTGAACCGGGGCATGGTACATTAAACCAAGTTGACCTAAACGTGATTTTCAAGTTTACGGA

Reverse complement sequence

TCCGTAAACTTGAAAATCACGTTTAGGTCAACTTGGTTTAATGTACCATGCCCCGGTTCAATAGCCCTTTGACTACTGCGATTAACTGCCAACCTAGCGC[T/A,G]
CCACGTAGGCAACACTTTTGCACTCGGCCCTCTCCGCATTACAGCATTTCACAAATATTGCCTATACCCCCCCTCAAGACACTGTAGCAACCCGAACCCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.20% 10.70% 0.11% 0.00% C: 0.04%
All Indica  2759 90.20% 9.60% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 17.10% 82.90% 0.00% 0.00% NA
Indica I  595 85.00% 14.60% 0.34% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 89.20% 10.80% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 8.80% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 85.60% 12.20% 0.00% 0.00% C: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0324719195 A -> T LOC_Os03g44000.1 upstream_gene_variant ; 2033.0bp to feature; MODIFIER silent_mutation Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63 N N N N
vg0324719195 A -> T LOC_Os03g43990-LOC_Os03g44000 intergenic_region ; MODIFIER silent_mutation Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63 N N N N
vg0324719195 A -> C LOC_Os03g44000.1 upstream_gene_variant ; 2033.0bp to feature; MODIFIER silent_mutation Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63 N N N N
vg0324719195 A -> C LOC_Os03g43990-LOC_Os03g44000 intergenic_region ; MODIFIER silent_mutation Average:60.071; most accessible tissue: Zhenshan97 root, score: 78.63 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324719195 NA 2.85E-06 mr1207 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
vg0324719195 NA 4.10E-06 mr1522_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
vg0324719195 1.15E-06 1.15E-06 mr1634_2 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