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Detailed information for vg1107084984:

Variant ID: vg1107084984 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7084984
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAGACAGAAGAGAGCGAGACGATGGAGAAGAGAGCGAAACGAGAGAGGGAGAGAAGAGGGAGCGAGACAAATCGACGATGAGAGCGAGACGTCGAACCT[T/G]
ATTCGATGCTCGTCTTGTGTGGGGGCCACCGGTCGGCTCATCCGATGCCGGCTCGGCTCGATTCACATAGGTGTCGGTTTTTTAACCGACACCTATAATA

Reverse complement sequence

TATTATAGGTGTCGGTTAAAAAACCGACACCTATGTGAATCGAGCCGAGCCGGCATCGGATGAGCCGACCGGTGGCCCCCACACAAGACGAGCATCGAAT[A/C]
AGGTTCGACGTCTCGCTCTCATCGTCGATTTGTCTCGCTCCCTCTTCTCTCCCTCTCTCGTTTCGCTCTCTTCTCCATCGTCTCGCTCTCTTCTGTCTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 3.90% 2.18% 1.14% NA
All Indica  2759 99.90% 0.00% 0.11% 0.00% NA
All Japonica  1512 78.00% 12.10% 6.42% 3.51% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 65.30% 21.30% 7.95% 5.48% NA
Tropical Japonica  504 95.80% 0.00% 2.98% 1.19% NA
Japonica Intermediate  241 80.90% 8.30% 8.71% 2.07% NA
VI/Aromatic  96 96.90% 0.00% 2.08% 1.04% NA
Intermediate  90 97.80% 1.10% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1107084984 T -> DEL N N silent_mutation Average:54.866; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg1107084984 T -> G LOC_Os11g12610.1 upstream_gene_variant ; 195.0bp to feature; MODIFIER silent_mutation Average:54.866; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg1107084984 T -> G LOC_Os11g12610-LOC_Os11g12620 intergenic_region ; MODIFIER silent_mutation Average:54.866; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107084984 3.23E-06 3.22E-06 mr1030 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
vg1107084984 NA 5.10E-06 mr1318 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
vg1107084984 NA 6.98E-07 mr1358 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
vg1107084984 8.08E-06 1.26E-06 mr1380 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
vg1107084984 NA 2.19E-06 mr1521 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
vg1107084984 NA 4.90E-06 mr1576 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
vg1107084984 NA 1.26E-06 mr1788 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
vg1107084984 NA 7.09E-06 mr1937 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
vg1107084984 NA 6.06E-07 mr1305_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
vg1107084984 NA 2.17E-09 mr1585_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
vg1107084984 NA 5.55E-06 mr1703_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
vg1107084984 NA 6.43E-06 mr1793_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