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Detailed information for vg1221072081:

Variant ID: vg1221072081 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21072081
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.02, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGTTCTCTCTCTCTCTCTTGCAAATTCAGATTTCAGAAATTACCGATGACTAGTAAGGTGAAAGTATTTCTTGCATTATAAATTCTGAATAATGTTTT[G/T]
CTTCAGTACTTGTTACTACTTACAATTAATAATAGAAAGAACATTAATGGGTGTTCAACAAACTGTACGGAGACAGATATATTAGTGAGCCATCGACATT

Reverse complement sequence

AATGTCGATGGCTCACTAATATATCTGTCTCCGTACAGTTTGTTGAACACCCATTAATGTTCTTTCTATTATTAATTGTAAGTAGTAACAAGTACTGAAG[C/A]
AAAACATTATTCAGAATTTATAATGCAAGAAATACTTTCACCTTACTAGTCATCGGTAATTTCTGAAATCTGAATTTGCAAGAGAGAGAGAGAGAACTTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.80% 29.10% 0.21% 29.92% NA
All Indica  2759 48.10% 9.10% 0.18% 42.55% NA
All Japonica  1512 32.10% 66.10% 0.13% 1.65% NA
Aus  269 3.00% 26.00% 1.12% 69.89% NA
Indica I  595 79.70% 11.90% 0.00% 8.40% NA
Indica II  465 44.90% 12.70% 0.00% 42.37% NA
Indica III  913 31.40% 2.60% 0.11% 65.83% NA
Indica Intermediate  786 45.50% 12.50% 0.51% 41.48% NA
Temperate Japonica  767 5.90% 93.40% 0.13% 0.65% NA
Tropical Japonica  504 75.40% 21.20% 0.20% 3.17% NA
Japonica Intermediate  241 24.90% 73.40% 0.00% 1.66% NA
VI/Aromatic  96 70.80% 16.70% 0.00% 12.50% NA
Intermediate  90 43.30% 40.00% 0.00% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1221072081 G -> DEL N N silent_mutation Average:34.335; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg1221072081 G -> T LOC_Os12g34700.1 downstream_gene_variant ; 3423.0bp to feature; MODIFIER silent_mutation Average:34.335; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg1221072081 G -> T LOC_Os12g34710.1 downstream_gene_variant ; 326.0bp to feature; MODIFIER silent_mutation Average:34.335; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg1221072081 G -> T LOC_Os12g34700-LOC_Os12g34710 intergenic_region ; MODIFIER silent_mutation Average:34.335; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221072081 NA 1.39E-06 mr1013 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
vg1221072081 NA 3.15E-06 mr1034 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
vg1221072081 NA 6.99E-08 mr1045 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
vg1221072081 NA 1.09E-06 mr1090 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
vg1221072081 NA 1.43E-10 mr1093 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
vg1221072081 NA 3.46E-06 mr1094 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
vg1221072081 NA 2.79E-06 mr1096 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
vg1221072081 7.77E-06 NA mr1120 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
vg1221072081 1.55E-06 4.62E-08 mr1120 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
vg1221072081 NA 7.02E-07 mr1121 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
vg1221072081 NA 3.12E-10 mr1235 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
vg1221072081 NA 9.89E-07 mr1257 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
vg1221072081 3.08E-08 NA mr1334 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
vg1221072081 2.75E-09 1.16E-24 mr1334 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
vg1221072081 NA 9.31E-11 mr1435 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
vg1221072081 NA 1.34E-08 mr1599 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
vg1221072081 NA 8.58E-06 mr1603 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
vg1221072081 NA 3.74E-06 mr1642 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
vg1221072081 NA 8.26E-10 mr1790 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
vg1221072081 9.49E-10 NA mr1334_2 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
vg1221072081 1.65E-08 3.15E-29 mr1334_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
vg1221072081 NA 5.65E-08 mr1817_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
vg1221072081 NA 1.62E-12 mr1991_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