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Detailed information for vg1108842350:

Variant ID: vg1108842350 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 8842350
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTACTCATTGCTAATTGAACCAGGAAGTAAAGACACATGATCTCAATTCTCTGCATACAAATCACAAAAATATGCCTTGAACTGAACTGAGTTTACT[C/T]
ATTCTAGGTTTCAACTTTTCAATTAATCTCACTCTGCTAAGAGAAAAACCAAACCAGAGAGAGATCCTAGAAATACTCACTGAATATACCAGCCGTCAGC

Reverse complement sequence

GCTGACGGCTGGTATATTCAGTGAGTATTTCTAGGATCTCTCTCTGGTTTGGTTTTTCTCTTAGCAGAGTGAGATTAATTGAAAAGTTGAAACCTAGAAT[G/A]
AGTAAACTCAGTTCAGTTCAAGGCATATTTTTGTGATTTGTATGCAGAGAATTGAGATCATGTGTCTTTACTTCCTGGTTCAATTAGCAATGAGTAAAAA

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 98.70% 1.30% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.00% 4.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 90.10% 9.70% 0.20% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg1108842350 C -> T LOC_Os11g15580.1 downstream_gene_variant ; 4665.0bp to feature; MODIFIER silent_mutation Average:17.433; most accessible tissue: Zhenshan97 panicle, score: 36.038 N N N N
vg1108842350 C -> T LOC_Os11g15590.1 intron_variant ; MODIFIER silent_mutation Average:17.433; most accessible tissue: Zhenshan97 panicle, score: 36.038 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1108842350 NA 4.14E-07 mr1136 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
vg1108842350 NA 6.61E-08 mr1188 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
vg1108842350 NA 3.02E-06 mr1583 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
vg1108842350 NA 1.61E-09 mr1188_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
vg1108842350 1.75E-06 3.42E-10 mr1218_2 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
vg1108842350 NA 2.41E-09 mr1850_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