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Detailed information for vg1112018736:

Variant ID: vg1112018736 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 12018736
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


TCCAGACCCCAAGTAAAACTGTTTGGACGGCCCACTATCCTTCTTTAGTTTGAAACGTGAGACAGGAAACCGACCAAACTCCTCGACTCCCCTAGGTTGT[C/T]
ATGTTTCCAGCCGGCCGGTTGTACTCCCAAAGATCAACTCTCTTCTTTCTTCCTCCGTCGCCAAAAAAACTTCCTTGTCATCCTCCTCCCTCAAACCTGC

Reverse complement sequence

GCAGGTTTGAGGGAGGAGGATGACAAGGAAGTTTTTTTGGCGACGGAGGAAGAAAGAAGAGAGTTGATCTTTGGGAGTACAACCGGCCGGCTGGAAACAT[G/A]
ACAACCTAGGGGAGTCGAGGAGTTTGGTCGGTTTCCTGTCTCACGTTTCAAACTAAAGAAGGATAGTGGGCCGTCCAAACAGTTTTACTTGGGGTCTGGA

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 93.70% 3.30% 3.00% 0.00% NA
All Indica  2759 89.40% 5.60% 5.00% 0.00% NA
All Japonica  1512 99.80% 0.00% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 61.80% 20.80% 17.31% 0.00% NA
Indica II  465 97.20% 0.60% 2.15% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 3.60% 3.18% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 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 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
vg1112018736 C -> T LOC_Os11g20770.1 upstream_gene_variant ; 2425.0bp to feature; MODIFIER silent_mutation Average:37.679; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg1112018736 C -> T LOC_Os11g20780.1 upstream_gene_variant ; 4876.0bp to feature; MODIFIER silent_mutation Average:37.679; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N
vg1112018736 C -> T LOC_Os11g20760.1 intron_variant ; MODIFIER silent_mutation Average:37.679; most accessible tissue: Minghui63 young leaf, score: 61.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1112018736 NA 8.66E-10 mr1038 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
vg1112018736 2.84E-06 NA mr1141 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
vg1112018736 7.02E-06 3.84E-10 mr1389 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
vg1112018736 2.16E-07 2.95E-11 mr1038_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
vg1112018736 3.03E-07 9.09E-12 mr1389_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