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Detailed information for vg0401293960:

Variant ID: vg0401293960 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1293960
Reference Allele: AAlternative Allele: T,G
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGACCGCCAAACCAAAGTTGCATATTTCATCGCAGTCAAAACCACTTATCCCGGCAGTAAGTTGGCAGAATTATACTTTGCTAGGATAGTTTGTCTTC[A/T,G]
TGGAGTACCGAAGAGAATCGTCTCCGATCGGGGTAGCCAATTCACTACTAAGTTCTGGCAGAAATTGCAGGAAGAAATGGGAACTCATTTGAACTTTAGC

Reverse complement sequence

GCTAAAGTTCAAATGAGTTCCCATTTCTTCCTGCAATTTCTGCCAGAACTTAGTAGTGAATTGGCTACCCCGATCGGAGACGATTCTCTTCGGTACTCCA[T/A,C]
GAAGACAAACTATCCTAGCAAAGTATAATTCTGCCAACTTACTGCCGGGATAAGTGGTTTTGACTGCGATGAAATATGCAACTTTGGTTTGGCGGTCGAT

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 49.10% 5.90% 2.54% 42.36% G: 0.13%
All Indica  2759 44.30% 6.40% 2.97% 46.14% G: 0.22%
All Japonica  1512 56.20% 0.40% 1.52% 41.87% NA
Aus  269 66.90% 28.60% 4.09% 0.37% NA
Indica I  595 72.40% 0.00% 1.68% 25.38% G: 0.50%
Indica II  465 27.10% 3.40% 3.66% 65.59% G: 0.22%
Indica III  913 33.40% 12.00% 3.94% 50.60% NA
Indica Intermediate  786 45.80% 6.40% 2.42% 45.17% G: 0.25%
Temperate Japonica  767 56.50% 0.10% 2.22% 41.20% NA
Tropical Japonica  504 66.90% 0.20% 0.40% 32.54% NA
Japonica Intermediate  241 33.20% 1.70% 1.66% 63.49% NA
VI/Aromatic  96 17.70% 10.40% 3.12% 68.75% NA
Intermediate  90 57.80% 8.90% 1.11% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0401293960 A -> DEL N N silent_mutation Average:15.155; most accessible tissue: Callus, score: 60.966 N N N N
vg0401293960 A -> G LOC_Os04g03120.1 downstream_gene_variant ; 1669.0bp to feature; MODIFIER silent_mutation Average:15.155; most accessible tissue: Callus, score: 60.966 N N N N
vg0401293960 A -> G LOC_Os04g03110.1 intron_variant ; MODIFIER silent_mutation Average:15.155; most accessible tissue: Callus, score: 60.966 N N N N
vg0401293960 A -> T LOC_Os04g03120.1 downstream_gene_variant ; 1669.0bp to feature; MODIFIER silent_mutation Average:15.155; most accessible tissue: Callus, score: 60.966 N N N N
vg0401293960 A -> T LOC_Os04g03110.1 intron_variant ; MODIFIER silent_mutation Average:15.155; most accessible tissue: Callus, score: 60.966 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401293960 NA 9.54E-07 mr1735 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
vg0401293960 4.83E-06 NA mr1741 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
vg0401293960 6.90E-06 NA mr1549_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
vg0401293960 NA 7.79E-06 mr1735_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