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Detailed information for vg1117444694:

Variant ID: vg1117444694 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17444694
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


CGGTCTAAACGGCAACTCACCGGCAGTCAGACCGACTGCAAGGCGACGGTCAGACCGATGAGGTAGCAGCGGTCAGACCGGCGGTGACAACAGGCGACGG[C/T]
GACAAATTTCGGCGGTTAGACCAGAAGATCAACACTGGTCAGACCGGCGGCTACGCTTCGGTCAGACCGGTTAATCTATTCCGGTCAGATCGCAGATCAT

Reverse complement sequence

ATGATCTGCGATCTGACCGGAATAGATTAACCGGTCTGACCGAAGCGTAGCCGCCGGTCTGACCAGTGTTGATCTTCTGGTCTAACCGCCGAAATTTGTC[G/A]
CCGTCGCCTGTTGTCACCGCCGGTCTGACCGCTGCTACCTCATCGGTCTGACCGTCGCCTTGCAGTCGGTCTGACTGCCGGTGAGTTGCCGTTTAGACCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.30% 23.40% 0.13% 2.18% NA
All Indica  2759 70.10% 29.90% 0.00% 0.00% NA
All Japonica  1512 92.30% 0.50% 0.40% 6.75% NA
Aus  269 12.60% 87.40% 0.00% 0.00% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 68.80% 31.20% 0.00% 0.00% NA
Indica III  913 59.00% 41.00% 0.00% 0.00% NA
Indica Intermediate  786 66.00% 34.00% 0.00% 0.00% NA
Temperate Japonica  767 85.50% 0.40% 0.78% 13.30% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117444694 C -> T LOC_Os11g30000.1 intron_variant ; MODIFIER silent_mutation Average:39.333; most accessible tissue: Minghui63 flag leaf, score: 71.116 N N N N
vg1117444694 C -> DEL N N silent_mutation Average:39.333; most accessible tissue: Minghui63 flag leaf, score: 71.116 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117444694 NA 5.69E-07 mr1170 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
vg1117444694 NA 5.72E-07 mr1671 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
vg1117444694 NA 9.39E-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
vg1117444694 NA 8.61E-06 mr1807 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
vg1117444694 NA 3.36E-06 mr1931 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
vg1117444694 NA 4.11E-08 mr1958 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