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Detailed information for vg1217884118:

Variant ID: vg1217884118 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17884118
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTGACTTTTACTTTGCACATTTTAATTTTTGGAGGCTTTCACAAGGATTTTAATTATTCTAGGCATAATTTAAAGGATATATTTTAGAGTCGTTTTGG[A/G]
ACGTGACACTCTTGGGGCACGATTTTCTCCTAGATCATACGATCTATAATACACTCGGCGGATCAATCCCCGTATAGGAGTAGGGTATTACTTCTTATTA

Reverse complement sequence

TAATAAGAAGTAATACCCTACTCCTATACGGGGATTGATCCGCCGAGTGTATTATAGATCGTATGATCTAGGAGAAAATCGTGCCCCAAGAGTGTCACGT[T/C]
CCAAAACGACTCTAAAATATATCCTTTAAATTATGCCTAGAATAATTAAAATCCTTGTGAAAGCCTCCAAAAATTAAAATGTGCAAAGTAAAAGTCAAAC

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 49.90% 15.00% 0.30% 34.79% NA
All Indica  2759 61.00% 1.80% 0.36% 36.79% NA
All Japonica  1512 28.90% 41.80% 0.26% 29.03% NA
Aus  269 61.30% 0.00% 0.00% 38.66% NA
Indica I  595 95.80% 2.20% 0.00% 2.02% NA
Indica II  465 32.00% 4.50% 0.22% 63.23% NA
Indica III  913 51.30% 0.00% 0.44% 48.30% NA
Indica Intermediate  786 63.10% 2.20% 0.64% 34.10% NA
Temperate Japonica  767 24.90% 72.80% 0.00% 2.35% NA
Tropical Japonica  504 38.10% 2.80% 0.60% 58.53% NA
Japonica Intermediate  241 22.40% 24.90% 0.41% 52.28% NA
VI/Aromatic  96 37.50% 1.00% 0.00% 61.46% NA
Intermediate  90 43.30% 26.70% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217884118 A -> DEL N N silent_mutation Average:17.3; most accessible tissue: Zhenshan97 root, score: 38.035 N N N N
vg1217884118 A -> G LOC_Os12g29910.1 downstream_gene_variant ; 3159.0bp to feature; MODIFIER silent_mutation Average:17.3; most accessible tissue: Zhenshan97 root, score: 38.035 N N N N
vg1217884118 A -> G LOC_Os12g29920.1 intron_variant ; MODIFIER silent_mutation Average:17.3; most accessible tissue: Zhenshan97 root, score: 38.035 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217884118 NA 6.76E-12 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1217884118 NA 4.74E-09 mr1002 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
vg1217884118 NA 1.04E-07 mr1002 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
vg1217884118 NA 4.23E-11 mr1137 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
vg1217884118 NA 1.84E-08 mr1163 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
vg1217884118 NA 1.72E-06 mr1183 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
vg1217884118 NA 4.47E-06 mr1503 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
vg1217884118 NA 6.20E-09 mr1617 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
vg1217884118 NA 2.24E-06 mr1826 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
vg1217884118 NA 1.25E-07 mr1942 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
vg1217884118 NA 3.10E-06 mr1942 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
vg1217884118 NA 7.62E-08 mr1002_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
vg1217884118 NA 1.81E-21 mr1010_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
vg1217884118 NA 1.47E-08 mr1010_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
vg1217884118 NA 2.99E-06 mr1011_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
vg1217884118 NA 1.37E-06 mr1013_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
vg1217884118 NA 1.56E-32 mr1137_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
vg1217884118 NA 4.42E-10 mr1137_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
vg1217884118 NA 4.61E-07 mr1180_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
vg1217884118 NA 2.69E-07 mr1229_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
vg1217884118 NA 6.26E-06 mr1555_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
vg1217884118 NA 5.66E-06 mr1617_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
vg1217884118 NA 3.66E-11 mr1748_2 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
vg1217884118 NA 4.79E-07 mr1880_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