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Detailed information for vg1217240367:

Variant ID: vg1217240367 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17240367
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCTGGACAACGACTTGAGGACGTTCTTCACCGTTGCCAGAGTTAGCCTAGATATGCCCCTATGCATCTACCAGATCTACATGTGAAGGGGCATGAGGA[A/T]
GCAGATAACTAAGGTGACGTTGCATCCTTTCGCCATAGCTCGAGGTCTAGCATGATGATAAAGTCACTATTCTAGGGATTAGAGTTGGCGGCATGTTCTT

Reverse complement sequence

AAGAACATGCCGCCAACTCTAATCCCTAGAATAGTGACTTTATCATCATGCTAGACCTCGAGCTATGGCGAAAGGATGCAACGTCACCTTAGTTATCTGC[T/A]
TCCTCATGCCCCTTCACATGTAGATCTGGTAGATGCATAGGGGCATATCTAGGCTAACTCTGGCAACGGTGAAGAACGTCCTCAAGTCGTTGTCCAGGGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.50% 20.10% 5.35% 1.99% NA
All Indica  2759 60.80% 27.40% 8.48% 3.33% NA
All Japonica  1512 89.90% 9.50% 0.53% 0.00% NA
Aus  269 97.80% 0.70% 1.12% 0.37% NA
Indica I  595 65.40% 11.30% 16.97% 6.39% NA
Indica II  465 83.20% 12.30% 2.80% 1.72% NA
Indica III  913 42.60% 50.30% 4.93% 2.19% NA
Indica Intermediate  786 65.30% 21.90% 9.54% 3.31% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 73.20% 25.60% 1.19% 0.00% NA
Japonica Intermediate  241 94.20% 5.00% 0.83% 0.00% NA
VI/Aromatic  96 67.70% 26.00% 5.21% 1.04% NA
Intermediate  90 67.80% 28.90% 3.33% 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
vg1217240367 A -> DEL N N silent_mutation Average:33.277; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N
vg1217240367 A -> T LOC_Os12g29120.1 upstream_gene_variant ; 2287.0bp to feature; MODIFIER silent_mutation Average:33.277; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N
vg1217240367 A -> T LOC_Os12g29130.1 downstream_gene_variant ; 4393.0bp to feature; MODIFIER silent_mutation Average:33.277; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N
vg1217240367 A -> T LOC_Os12g29120-LOC_Os12g29130 intergenic_region ; MODIFIER silent_mutation Average:33.277; most accessible tissue: Minghui63 young leaf, score: 77.243 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217240367 NA 4.85E-07 mr1015 Ind_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
vg1217240367 NA 1.25E-06 mr1076 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
vg1217240367 NA 1.58E-06 mr1082 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
vg1217240367 2.09E-08 5.72E-11 mr1083 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
vg1217240367 NA 6.97E-06 mr1086 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
vg1217240367 3.87E-07 3.89E-09 mr1226 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
vg1217240367 NA 4.70E-07 mr1364 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
vg1217240367 NA 5.12E-06 mr1408 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
vg1217240367 4.75E-06 NA mr1437 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
vg1217240367 NA 2.81E-07 mr1443 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
vg1217240367 NA 9.56E-07 mr1471 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
vg1217240367 NA 6.45E-06 mr1653 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
vg1217240367 NA 3.26E-06 mr1949 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
vg1217240367 1.08E-09 1.08E-09 mr1076_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
vg1217240367 1.71E-06 2.97E-10 mr1083_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
vg1217240367 NA 4.47E-06 mr1092_2 Ind_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
vg1217240367 NA 1.61E-06 mr1103_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
vg1217240367 6.86E-08 1.83E-09 mr1104_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
vg1217240367 2.56E-07 1.16E-08 mr1107_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
vg1217240367 6.51E-07 2.59E-10 mr1226_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
vg1217240367 7.83E-07 7.83E-07 mr1264_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
vg1217240367 NA 5.88E-08 mr1408_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