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Detailed information for vg0400960642:

Variant ID: vg0400960642 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 960642
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTGGTCAAAATTTGTTAAGTTTTCAAATAATTTTGGACAAAAAAGTTCTAAGTTATACAAAAATTTTGGAAATCCCGGCAACGTTCGTTTTAAGAAAAT[A/T]
TTGTGCCCCGGAAATTTTGAACCTAGAGTAAGTTAGTGTGTGTAAGAATATAATGATTTTCACATAATATTGCATCATATTATCTAGGCAGTTTATGTAG

Reverse complement sequence

CTACATAAACTGCCTAGATAATATGATGCAATATTATGTGAAAATCATTATATTCTTACACACACTAACTTACTCTAGGTTCAAAATTTCCGGGGCACAA[T/A]
ATTTTCTTAAAACGAACGTTGCCGGGATTTCCAAAATTTTTGTATAACTTAGAACTTTTTTGTCCAAAATTATTTGAAAACTTAACAAATTTTGACCAAT

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 94.80% 5.20% 0.06% 0.00% NA
All Indica  2759 99.10% 0.80% 0.11% 0.00% NA
All Japonica  1512 89.70% 10.30% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 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 98.00% 1.80% 0.22% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 88.00% 12.00% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 78.40% 21.60% 0.00% 0.00% NA
VI/Aromatic  96 38.50% 61.50% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0400960642 A -> T LOC_Os04g02560.1 upstream_gene_variant ; 601.0bp to feature; MODIFIER silent_mutation Average:21.975; most accessible tissue: Minghui63 root, score: 27.443 N N N N
vg0400960642 A -> T LOC_Os04g02560-LOC_Os04g02570 intergenic_region ; MODIFIER silent_mutation Average:21.975; most accessible tissue: Minghui63 root, score: 27.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400960642 1.02E-06 NA mr1667_2 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