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Detailed information for vg0407887014:

Variant ID: vg0407887014 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7887014
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTTTGTCTAAACCAGCTACCACTCCATTTATAAGAGACATTATCCACATATACTTCAAATACAATTTTCTCTTAAACTACTCATCCAATTTACGATTCG[A/G]
TTGCACCGTTATGTTTGTAACAATTAATATTTATAACAAGATCTCACATGATTATATTCTGATAAAAAAATATAAATTACTTTTATAATATATCTAAATT

Reverse complement sequence

AATTTAGATATATTATAAAAGTAATTTATATTTTTTTATCAGAATATAATCATGTGAGATCTTGTTATAAATATTAATTGTTACAAACATAACGGTGCAA[T/C]
CGAATCGTAAATTGGATGAGTAGTTTAAGAGAAAATTGTATTTGAAGTATATGTGGATAATGTCTCTTATAAATGGAGTGGTAGCTGGTTTAGACAAACT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.70% 9.80% 0.80% 0.66% NA
All Indica  2759 99.50% 0.30% 0.07% 0.07% NA
All Japonica  1512 66.90% 29.00% 2.18% 1.85% 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 98.70% 0.90% 0.00% 0.43% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 99.40% 0.50% 0.13% 0.00% NA
Temperate Japonica  767 96.50% 3.00% 0.39% 0.13% NA
Tropical Japonica  504 18.10% 72.20% 5.56% 4.17% NA
Japonica Intermediate  241 75.10% 21.60% 0.83% 2.49% NA
VI/Aromatic  96 93.80% 4.20% 2.08% 0.00% NA
Intermediate  90 83.30% 14.40% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0407887014 A -> DEL N N silent_mutation Average:31.29; most accessible tissue: Minghui63 root, score: 46.493 N N N N
vg0407887014 A -> G LOC_Os04g14110.1 downstream_gene_variant ; 3860.0bp to feature; MODIFIER silent_mutation Average:31.29; most accessible tissue: Minghui63 root, score: 46.493 N N N N
vg0407887014 A -> G LOC_Os04g14110-LOC_Os04g14130 intergenic_region ; MODIFIER silent_mutation Average:31.29; most accessible tissue: Minghui63 root, score: 46.493 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407887014 NA 9.08E-06 mr1047 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
vg0407887014 NA 1.18E-23 mr1301 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
vg0407887014 NA 5.73E-14 mr1410 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
vg0407887014 NA 5.87E-13 mr1449 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
vg0407887014 NA 4.91E-14 mr1454 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
vg0407887014 1.74E-06 5.74E-12 mr1454 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
vg0407887014 NA 2.14E-06 mr1527 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
vg0407887014 NA 2.27E-06 mr1543 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
vg0407887014 NA 8.11E-07 mr1642 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
vg0407887014 NA 1.05E-08 mr1648 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
vg0407887014 NA 1.29E-11 mr1871 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
vg0407887014 NA 3.17E-23 mr1301_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
vg0407887014 NA 3.82E-15 mr1410_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
vg0407887014 NA 9.81E-10 mr1543_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
vg0407887014 NA 6.76E-09 mr1543_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
vg0407887014 NA 1.31E-13 mr1742_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
vg0407887014 NA 1.50E-10 mr1993_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