Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1204382187:

Variant ID: vg1204382187 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4382187
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.81, G: 0.19, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:


TTACTCCAGCCTCTTCAGATCCCGGAATGGAAATGGGAGGAGATTGGAATGGACTTTATAACAGGACTGCCCTGGACATCATCTGGCCACGATTCAATCT[A/G]
GGTAGTCGTGGATCGACTCACTAAAGTTGCTCATTTCATTCCAGTGCATACCACATATACGGGGAAGAAATTGGCAGAGCTGTACCTGACAAGGATCATG

Reverse complement sequence

CATGATCCTTGTCAGGTACAGCTCTGCCAATTTCTTCCCCGTATATGTGGTATGCACTGGAATGAAATGAGCAACTTTAGTGAGTCGATCCACGACTACC[T/C]
AGATTGAATCGTGGCCAGATGATGTCCAGGGCAGTCCTGTTATAAAGTCCATTCCAATCTCCTCCCATTTCCATTCCGGGATCTGAAGAGGCTGGAGTAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 31.50% 0.20% 2.79% 65.53% NA
All Indica  2759 19.40% 0.30% 2.50% 77.85% NA
All Japonica  1512 55.20% 0.10% 3.90% 40.87% NA
Aus  269 25.70% 0.00% 1.12% 73.23% NA
Indica I  595 33.10% 0.20% 5.55% 61.18% NA
Indica II  465 27.10% 0.40% 1.29% 71.18% NA
Indica III  913 3.00% 0.10% 1.10% 95.84% NA
Indica Intermediate  786 23.50% 0.40% 2.54% 73.54% NA
Temperate Japonica  767 80.20% 0.10% 5.48% 14.21% NA
Tropical Japonica  504 27.40% 0.00% 0.99% 71.63% NA
Japonica Intermediate  241 33.60% 0.00% 4.98% 61.41% NA
VI/Aromatic  96 15.60% 0.00% 0.00% 84.38% NA
Intermediate  90 40.00% 0.00% 1.11% 58.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1204382187 A -> DEL N N silent_mutation Average:19.109; most accessible tissue: Callus, score: 49.112 N N N N
vg1204382187 A -> G LOC_Os12g08610.1 downstream_gene_variant ; 3591.0bp to feature; MODIFIER silent_mutation Average:19.109; most accessible tissue: Callus, score: 49.112 N N N N
vg1204382187 A -> G LOC_Os12g08620.1 intron_variant ; MODIFIER silent_mutation Average:19.109; most accessible tissue: Callus, score: 49.112 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204382187 NA 1.33E-06 mr1668 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
vg1204382187 NA 2.86E-06 mr1133_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
vg1204382187 NA 1.04E-07 mr1308_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
vg1204382187 NA 1.71E-08 mr1401_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
vg1204382187 NA 1.79E-06 mr1422_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
vg1204382187 NA 1.39E-07 mr1606_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
vg1204382187 NA 1.77E-08 mr1696_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
vg1204382187 NA 2.85E-06 mr1819_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
vg1204382187 NA 9.89E-07 mr1853_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
vg1204382187 NA 5.46E-06 mr1866_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
vg1204382187 NA 1.97E-06 mr1888_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
vg1204382187 NA 3.30E-07 mr1905_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
vg1204382187 NA 5.56E-10 mr1942_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