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Detailed information for vg0721070602:

Variant ID: vg0721070602 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21070602
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGATATTCCGAAAGATTTTCGGACATGTTCGAAAATTCCAGCTCAGCACCGACAGCAAAGTCAACGAAGTATTTTTCGGACATTCCGAAAACTTTTCG[G/A]
ACAAGTCCGAAAACAACAACATCGTTCTGGATGTTCTCGGAAAAGTCCGAAAATCACTTTCGGACAAGTTCGAAAATATACAGAAGCGAAATTGACTCTA

Reverse complement sequence

TAGAGTCAATTTCGCTTCTGTATATTTTCGAACTTGTCCGAAAGTGATTTTCGGACTTTTCCGAGAACATCCAGAACGATGTTGTTGTTTTCGGACTTGT[C/T]
CGAAAAGTTTTCGGAATGTCCGAAAAATACTTCGTTGACTTTGCTGTCGGTGCTGAGCTGGAATTTTCGAACATGTCCGAAAATCTTTCGGAATATCCGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.30% 8.90% 0.95% 47.80% NA
All Indica  2759 18.30% 3.70% 1.52% 76.44% NA
All Japonica  1512 78.70% 19.90% 0.00% 1.39% NA
Aus  269 75.50% 0.00% 0.00% 24.54% NA
Indica I  595 15.50% 0.20% 2.52% 81.85% NA
Indica II  465 19.10% 4.50% 1.51% 74.84% NA
Indica III  913 18.80% 7.00% 0.99% 73.17% NA
Indica Intermediate  786 19.50% 2.00% 1.40% 77.10% NA
Temperate Japonica  767 98.30% 0.80% 0.00% 0.91% NA
Tropical Japonica  504 45.80% 53.60% 0.00% 0.60% NA
Japonica Intermediate  241 85.10% 10.40% 0.00% 4.56% NA
VI/Aromatic  96 62.50% 3.10% 2.08% 32.29% NA
Intermediate  90 45.60% 17.80% 1.11% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0721070602 G -> DEL N N silent_mutation Average:10.385; most accessible tissue: Callus, score: 26.875 N N N N
vg0721070602 G -> A LOC_Os07g35190.1 upstream_gene_variant ; 2573.0bp to feature; MODIFIER silent_mutation Average:10.385; most accessible tissue: Callus, score: 26.875 N N N N
vg0721070602 G -> A LOC_Os07g35200.1 upstream_gene_variant ; 3638.0bp to feature; MODIFIER silent_mutation Average:10.385; most accessible tissue: Callus, score: 26.875 N N N N
vg0721070602 G -> A LOC_Os07g35180-LOC_Os07g35190 intergenic_region ; MODIFIER silent_mutation Average:10.385; most accessible tissue: Callus, score: 26.875 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721070602 NA 8.78E-07 mr1121 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
vg0721070602 NA 1.32E-08 mr1068_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
vg0721070602 NA 1.33E-06 mr1078_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
vg0721070602 NA 2.44E-08 mr1090_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
vg0721070602 NA 3.11E-06 mr1091_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
vg0721070602 NA 6.29E-06 mr1094_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
vg0721070602 NA 2.30E-08 mr1096_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
vg0721070602 NA 5.37E-07 mr1110_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
vg0721070602 NA 2.12E-06 mr1112_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
vg0721070602 8.98E-06 5.77E-10 mr1121_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
vg0721070602 NA 4.26E-06 mr1200_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
vg0721070602 NA 4.51E-08 mr1220_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
vg0721070602 NA 7.72E-06 mr1786_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
vg0721070602 NA 2.53E-07 mr1798_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
vg0721070602 NA 1.81E-06 mr1936_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