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Detailed information for vg0706185610:

Variant ID: vg0706185610 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 6185610
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCTCTTTTACATAAGTTGTCAACTAGGTTATTTCCCGATAATGAGATGTGGTAGATAGACCTTAATCATGACAAGGATGAAATGCATGGAGAAAAAGC[A/C]
ATATGTATCACTTCTTATCTCCTACTTTTTGATAGGTTCATATATATGATTTCCATGTTATTGTTATATAAGTGTGAGACTAATGTTTACTTGAGCATTA

Reverse complement sequence

TAATGCTCAAGTAAACATTAGTCTCACACTTATATAACAATAACATGGAAATCATATATATGAACCTATCAAAAAGTAGGAGATAAGAAGTGATACATAT[T/G]
GCTTTTTCTCCATGCATTTCATCCTTGTCATGATTAAGGTCTATCTACCACATCTCATTATCGGGAAATAACCTAGTTGACAACTTATGTAAAAGAGAGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.50% 5.80% 3.77% 3.87% NA
All Indica  2759 93.10% 0.40% 4.39% 2.14% NA
All Japonica  1512 80.20% 17.20% 2.65% 0.00% NA
Aus  269 51.30% 0.00% 3.72% 44.98% NA
Indica I  595 89.40% 0.20% 8.91% 1.51% NA
Indica II  465 93.80% 1.70% 4.52% 0.00% NA
Indica III  913 97.30% 0.00% 0.66% 2.08% NA
Indica Intermediate  786 90.70% 0.10% 5.22% 3.94% NA
Temperate Japonica  767 96.50% 0.70% 2.87% 0.00% NA
Tropical Japonica  504 48.40% 49.00% 2.58% 0.00% NA
Japonica Intermediate  241 94.60% 3.30% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 5.60% 7.78% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0706185610 A -> DEL N N silent_mutation Average:26.039; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0706185610 A -> C LOC_Os07g11230.1 upstream_gene_variant ; 2044.0bp to feature; MODIFIER silent_mutation Average:26.039; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0706185610 A -> C LOC_Os07g11240.1 upstream_gene_variant ; 1412.0bp to feature; MODIFIER silent_mutation Average:26.039; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0706185610 A -> C LOC_Os07g11230-LOC_Os07g11240 intergenic_region ; MODIFIER silent_mutation Average:26.039; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0706185610 NA 1.46E-06 mr1471 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
vg0706185610 NA 2.45E-07 mr1676 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
vg0706185610 NA 5.05E-07 mr1742 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
vg0706185610 2.02E-07 NA mr1083_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
vg0706185610 NA 3.27E-08 mr1304_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
vg0706185610 NA 6.40E-11 mr1364_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
vg0706185610 NA 7.23E-12 mr1364_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
vg0706185610 NA 2.65E-10 mr1408_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
vg0706185610 NA 2.91E-14 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
vg0706185610 NA 4.86E-13 mr1552_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
vg0706185610 NA 3.58E-06 mr1562_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
vg0706185610 NA 8.12E-08 mr1653_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
vg0706185610 NA 2.61E-08 mr1676_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
vg0706185610 NA 2.73E-10 mr1696_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
vg0706185610 NA 2.81E-07 mr1696_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
vg0706185610 NA 4.24E-10 mr1705_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
vg0706185610 NA 2.31E-07 mr1819_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
vg0706185610 NA 2.01E-10 mr1905_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
vg0706185610 NA 2.43E-07 mr1905_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
vg0706185610 NA 4.28E-09 mr1916_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
vg0706185610 NA 1.11E-11 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