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Detailed information for vg1107947407:

Variant ID: vg1107947407 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7947407
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GACGCAATAGTTCAAGGGCGGTAATTCGTACGTTTTCCTTTTGGATGAATATGACACTTCCTAGTACAATGAATTTGGACATACGGTCACATCCACCCAA[A/C]
ATCCCTTATATTATAGGACGAAGGGAATATCAGACGTTCGCTTCCACTCCTAAAACCCTGCCCGCACCTCACACCATCTTCATGGTGTCTGAGTTGCACC

Reverse complement sequence

GGTGCAACTCAGACACCATGAAGATGGTGTGAGGTGCGGGCAGGGTTTTAGGAGTGGAAGCGAACGTCTGATATTCCCTTCGTCCTATAATATAAGGGAT[T/G]
TTGGGTGGATGTGACCGTATGTCCAAATTCATTGTACTAGGAAGTGTCATATTCATCCAAAAGGAAAACGTACGAATTACCGCCCTTGAACTATTGCGTC

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 85.10% 14.90% 0.06% 0.00% NA
All Indica  2759 75.90% 24.10% 0.07% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 88.40% 11.30% 0.34% 0.00% NA
Indica II  465 76.60% 23.40% 0.00% 0.00% NA
Indica III  913 66.30% 33.70% 0.00% 0.00% NA
Indica Intermediate  786 77.10% 22.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 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
vg1107947407 A -> C LOC_Os11g14200.1 downstream_gene_variant ; 583.0bp to feature; MODIFIER silent_mutation Average:53.572; most accessible tissue: Zhenshan97 young leaf, score: 76.099 N N N N
vg1107947407 A -> C LOC_Os11g14200-LOC_Os11g14210 intergenic_region ; MODIFIER silent_mutation Average:53.572; most accessible tissue: Zhenshan97 young leaf, score: 76.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107947407 NA 9.74E-07 mr1498 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
vg1107947407 4.63E-06 4.63E-06 mr1640 Ind_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
vg1107947407 NA 9.49E-07 mr1729 Ind_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
vg1107947407 NA 9.86E-07 mr1925 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
vg1107947407 NA 3.71E-13 mr1951 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
vg1107947407 NA 5.42E-11 mr1951 Ind_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
vg1107947407 NA 5.88E-06 mr1956 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
vg1107947407 NA 7.94E-06 mr1956 Ind_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