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Detailed information for vg1204324436:

Variant ID: vg1204324436 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4324436
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


ATAACTCATTCCAAATTGATAGCACAACTGATACATATATCTCATCAAACACATTGTCTTTCCAGAGCATAGCTAACACATAATAAAGGACCTCATTACA[T/A]
CATATTGGCCACACATCACACTGTCTCACTTCTTGCCAAAGAACACCACAAATAGCACAAACATACATGACACCACACATATTACAAAGACTTTTCTTTC

Reverse complement sequence

GAAAGAAAAGTCTTTGTAATATGTGTGGTGTCATGTATGTTTGTGCTATTTGTGGTGTTCTTTGGCAAGAAGTGAGACAGTGTGATGTGTGGCCAATATG[A/T]
TGTAATGAGGTCCTTTATTATGTGTTAGCTATGCTCTGGAAAGACAATGTGTTTGATGAGATATATGTATCAGTTGTGCTATCAATTTGGAATGAGTTAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 27.40% 18.30% 0.97% 53.34% NA
All Indica  2759 7.90% 30.60% 1.27% 60.20% NA
All Japonica  1512 58.30% 0.40% 0.33% 40.94% NA
Aus  269 52.80% 0.00% 1.86% 45.35% NA
Indica I  595 9.20% 78.30% 1.34% 11.09% NA
Indica II  465 9.00% 9.90% 0.86% 80.22% NA
Indica III  913 2.70% 15.70% 1.53% 80.07% NA
Indica Intermediate  786 12.20% 24.20% 1.15% 62.47% NA
Temperate Japonica  767 84.10% 0.50% 0.26% 15.12% NA
Tropical Japonica  504 29.20% 0.20% 0.60% 70.04% NA
Japonica Intermediate  241 37.30% 0.40% 0.00% 62.24% NA
VI/Aromatic  96 17.70% 3.10% 0.00% 79.17% NA
Intermediate  90 37.80% 13.30% 1.11% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1204324436 T -> DEL N N silent_mutation Average:11.638; most accessible tissue: Callus, score: 33.41 N N N N
vg1204324436 T -> A LOC_Os12g08510.1 upstream_gene_variant ; 3688.0bp to feature; MODIFIER silent_mutation Average:11.638; most accessible tissue: Callus, score: 33.41 N N N N
vg1204324436 T -> A LOC_Os12g08530.1 downstream_gene_variant ; 26.0bp to feature; MODIFIER silent_mutation Average:11.638; most accessible tissue: Callus, score: 33.41 N N N N
vg1204324436 T -> A LOC_Os12g08510-LOC_Os12g08530 intergenic_region ; MODIFIER silent_mutation Average:11.638; most accessible tissue: Callus, score: 33.41 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204324436 8.42E-06 8.42E-06 mr1645 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
vg1204324436 4.78E-06 4.78E-06 mr1053_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
vg1204324436 2.27E-06 2.27E-06 mr1058_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
vg1204324436 7.69E-06 6.95E-06 mr1114_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
vg1204324436 8.22E-06 7.26E-06 mr1117_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
vg1204324436 2.27E-06 NA mr1118_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
vg1204324436 1.67E-06 1.80E-06 mr1119_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
vg1204324436 2.04E-06 4.56E-06 mr1120_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
vg1204324436 1.30E-06 NA mr1123_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
vg1204324436 3.46E-06 3.46E-06 mr1209_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
vg1204324436 1.16E-06 1.80E-06 mr1247_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
vg1204324436 9.32E-07 9.31E-07 mr1424_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
vg1204324436 7.48E-06 7.48E-06 mr1605_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
vg1204324436 1.10E-06 1.37E-06 mr1720_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
vg1204324436 9.71E-06 9.70E-06 mr1787_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
vg1204324436 NA 5.65E-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
vg1204324436 4.33E-06 4.33E-06 mr1820_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
vg1204324436 8.25E-06 1.75E-06 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
vg1204324436 3.15E-06 1.71E-06 mr1884_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
vg1204324436 2.39E-06 NA mr1936_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
vg1204324436 7.05E-06 7.05E-06 mr1960_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