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Detailed information for vg0407789423:

Variant ID: vg0407789423 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7789423
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTACTCCTTTGCATTTATGCTGCACTTGTGGGTGTGTCTTGTTGAGTATGGTGGTTGTACTCAGTCTTGCTCAATTTTTCCCAAACCCAGAAGAGGAG[G/C]
CCCTGGATGATGAAGGCTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCATCGCCTTAGTCTTCCGCTGTTTTTCGTTGTCTTTGAGTGTG

Reverse complement sequence

CACACTCAAAGACAACGAAAAACAGCGGAAGACTAAGGCGATGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAGCCTTCATCATCCAGGG[C/G]
CTCCTCTTCTGGGTTTGGGAAAAATTGAGCAAGACTGAGTACAACCACCATACTCAACAAGACACACCCACAAGTGCAGCATAAATGCAAAGGAGTACAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 30.00% 11.40% 3.55% 55.01% NA
All Indica  2759 11.80% 0.60% 4.97% 82.64% NA
All Japonica  1512 65.90% 32.80% 0.13% 1.19% NA
Aus  269 3.30% 0.40% 8.92% 87.36% NA
Indica I  595 18.50% 0.30% 5.88% 75.29% NA
Indica II  465 13.50% 1.30% 3.66% 81.51% NA
Indica III  913 2.40% 0.40% 3.50% 93.65% NA
Indica Intermediate  786 16.50% 0.60% 6.74% 76.08% NA
Temperate Japonica  767 96.30% 3.30% 0.00% 0.39% NA
Tropical Japonica  504 16.30% 81.30% 0.40% 1.98% NA
Japonica Intermediate  241 72.60% 25.30% 0.00% 2.07% NA
VI/Aromatic  96 55.20% 6.20% 4.17% 34.38% NA
Intermediate  90 41.10% 20.00% 1.11% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0407789423 G -> C LOC_Os04g13940.1 upstream_gene_variant ; 803.0bp to feature; MODIFIER silent_mutation Average:11.465; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0407789423 G -> C LOC_Os04g13950.1 upstream_gene_variant ; 4584.0bp to feature; MODIFIER silent_mutation Average:11.465; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0407789423 G -> C LOC_Os04g13930.1 downstream_gene_variant ; 2837.0bp to feature; MODIFIER silent_mutation Average:11.465; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0407789423 G -> C LOC_Os04g13930-LOC_Os04g13940 intergenic_region ; MODIFIER silent_mutation Average:11.465; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0407789423 G -> DEL N N silent_mutation Average:11.465; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407789423 NA 2.85E-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
vg0407789423 NA 6.75E-21 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
vg0407789423 NA 5.82E-14 mr1301 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
vg0407789423 NA 3.19E-07 mr1338 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
vg0407789423 NA 8.42E-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
vg0407789423 NA 2.84E-12 mr1454 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
vg0407789423 NA 1.42E-10 mr1454 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
vg0407789423 NA 2.63E-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
vg0407789423 NA 2.34E-08 mr1539 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
vg0407789423 NA 3.15E-12 mr1540 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
vg0407789423 NA 7.33E-13 mr1732 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
vg0407789423 NA 7.88E-24 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
vg0407789423 NA 2.69E-16 mr1301_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
vg0407789423 NA 1.12E-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
vg0407789423 NA 8.97E-13 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