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Detailed information for vg1118303285:

Variant ID: vg1118303285 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18303285
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ACACTTCATCCGTCTCTCTTTATTGTAGATGCCATCTATACCACGGTTGCACCTTAATAGACTATATGCGAACTGTTTTGCAGAAAAACAATGGCAGTCC[G/A]
TCTGCTGCCCATACTCATGCCCCTCTGGTGGAAACCATGGTCGAACCTGATAATTCTTGGATGATATGTCGCATTTACAAGAAGAGGCAGCGTGCACCGC

Reverse complement sequence

GCGGTGCACGCTGCCTCTTCTTGTAAATGCGACATATCATCCAAGAATTATCAGGTTCGACCATGGTTTCCACCAGAGGGGCATGAGTATGGGCAGCAGA[C/T]
GGACTGCCATTGTTTTTCTGCAAAACAGTTCGCATATAGTCTATTAAGGTGCAACCGTGGTATAGATGGCATCTACAATAAAGAGAGACGGATGAAGTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.60% 10.40% 0.02% 0.00% NA
All Indica  2759 99.40% 0.60% 0.00% 0.00% NA
All Japonica  1512 69.90% 30.10% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 94.70% 5.30% 0.00% 0.00% NA
Tropical Japonica  504 32.90% 67.10% 0.00% 0.00% NA
Japonica Intermediate  241 68.50% 31.50% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg1118303285 G -> A LOC_Os11g31360.1 synonymous_variant ; p.Pro185Pro; LOW synonymous_codon Average:41.607; most accessible tissue: Callus, score: 66.833 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118303285 NA 4.94E-06 mr1192 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
vg1118303285 2.74E-07 3.06E-17 mr1871 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
vg1118303285 NA 4.48E-07 mr1871 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
vg1118303285 NA 5.12E-06 mr1194_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