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Detailed information for vg0611426472:

Variant ID: vg0611426472 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11426472
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.14, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:


TGCACAGCACACCAGGGTTTAACTCACCGCCGGTAACCGCGCGGTTACCGCGGTTACCGGGCTTACCGCGGGGGTACGGTAATATAAATACCGTGGTAAC[T/C]
TCCTTAAATACAAATAAATTTAAAAAATAATTTGAATTTTTGATAAATTTTGCACGGTTTTGTACGGTTTTTCACGGTTACCGCGGTTACCGAGCGGTAA

Reverse complement sequence

TTACCGCTCGGTAACCGCGGTAACCGTGAAAAACCGTACAAAACCGTGCAAAATTTATCAAAAATTCAAATTATTTTTTAAATTTATTTGTATTTAAGGA[A/G]
GTTACCACGGTATTTATATTACCGTACCCCCGCGGTAAGCCCGGTAACCGCGGTAACCGCGCGGTTACCGGCGGTGAGTTAAACCCTGGTGTGCTGTGCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.80% 1.30% 0.68% 61.30% NA
All Indica  2759 4.30% 0.00% 0.72% 95.00% NA
All Japonica  1512 85.30% 4.00% 0.53% 10.25% NA
Aus  269 75.10% 0.00% 0.00% 24.91% NA
Indica I  595 7.20% 0.00% 0.50% 92.27% NA
Indica II  465 3.00% 0.00% 0.22% 96.77% NA
Indica III  913 1.30% 0.00% 1.10% 97.59% NA
Indica Intermediate  786 6.20% 0.00% 0.76% 93.00% NA
Temperate Japonica  767 90.40% 6.30% 0.13% 3.26% NA
Tropical Japonica  504 75.40% 0.80% 0.99% 22.82% NA
Japonica Intermediate  241 89.60% 3.30% 0.83% 6.22% NA
VI/Aromatic  96 85.40% 0.00% 1.04% 13.54% NA
Intermediate  90 51.10% 0.00% 3.33% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611426472 T -> C LOC_Os06g19940.1 upstream_gene_variant ; 4088.0bp to feature; MODIFIER silent_mutation Average:58.846; most accessible tissue: Minghui63 root, score: 78.833 N N N N
vg0611426472 T -> C LOC_Os06g19950.1 downstream_gene_variant ; 1537.0bp to feature; MODIFIER silent_mutation Average:58.846; most accessible tissue: Minghui63 root, score: 78.833 N N N N
vg0611426472 T -> C LOC_Os06g19950-LOC_Os06g19960 intergenic_region ; MODIFIER silent_mutation Average:58.846; most accessible tissue: Minghui63 root, score: 78.833 N N N N
vg0611426472 T -> DEL N N silent_mutation Average:58.846; most accessible tissue: Minghui63 root, score: 78.833 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611426472 NA 3.39E-06 mr1121 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
vg0611426472 NA 3.20E-42 mr1144 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
vg0611426472 NA 1.99E-09 mr1151 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
vg0611426472 NA 7.98E-42 mr1200 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
vg0611426472 9.59E-06 4.24E-06 mr1200 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
vg0611426472 NA 4.18E-08 mr1249 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
vg0611426472 NA 2.94E-06 mr1990 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
vg0611426472 NA 4.04E-09 mr1068_2 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
vg0611426472 6.10E-06 1.97E-10 mr1087_2 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
vg0611426472 NA 2.91E-08 mr1111_2 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
vg0611426472 NA 3.42E-09 mr1112_2 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
vg0611426472 NA 3.18E-06 mr1121_2 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
vg0611426472 2.06E-06 8.16E-11 mr1200_2 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
vg0611426472 NA 5.25E-07 mr1211_2 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
vg0611426472 NA 8.76E-08 mr1399_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