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Detailed information for vg1218054911:

Variant ID: vg1218054911 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 18054911
Reference Allele: GCTAlternative Allele: ACT,G
Primary Allele: GCTSecondary Allele: ACT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTATTAGATATAGACTACTTACAAAACTAATTACATAAATGAAAACTAATTCGCGAGACAAATATTTTAAGCCTAATTAATCCATAATTAGAGAATGTTT[GCT/ACT,G]
GTAGCATCACATAGGCTAATCATAGATTAATTAGGCTCAATAGATTCGTCTCACGAATTAGTCCAAGATTATGGATGGGTTTTATTAATAGTCTACGTTT

Reverse complement sequence

AAACGTAGACTATTAATAAAACCCATCCATAATCTTGGACTAATTCGTGAGACGAATCTATTGAGCCTAATTAATCTATGATTAGCCTATGTGATGCTAC[AGC/AGT,C]
AAACATTCTCTAATTATGGATTAATTAGGCTTAAAATATTTGTCTCGCGAATTAGTTTTCATTTATGTAATTAGTTTTGTAAGTAGTCTATATCTAATAC

Allele Frequencies:

Populations Population SizeFrequency of GCT(primary allele) Frequency of ACT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.90% 25.70% 0.13% 0.83% G: 0.47%
All Indica  2759 86.40% 11.30% 0.11% 1.41% G: 0.72%
All Japonica  1512 50.60% 49.10% 0.20% 0.00% G: 0.13%
Aus  269 73.60% 26.40% 0.00% 0.00% NA
Indica I  595 96.80% 2.90% 0.00% 0.00% G: 0.34%
Indica II  465 74.20% 25.40% 0.00% 0.43% NA
Indica III  913 85.40% 10.60% 0.00% 3.94% NA
Indica Intermediate  786 86.90% 10.30% 0.38% 0.13% G: 2.29%
Temperate Japonica  767 65.40% 34.00% 0.26% 0.00% G: 0.26%
Tropical Japonica  504 27.20% 72.60% 0.20% 0.00% NA
Japonica Intermediate  241 52.30% 47.70% 0.00% 0.00% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 0.00% 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
vg1218054911 GCT -> DEL N N silent_mutation Average:38.792; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg1218054911 GCT -> G LOC_Os12g30120-LOC_Os12g30130 intergenic_region ; MODIFIER silent_mutation Average:38.792; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg1218054911 GCT -> ACT LOC_Os12g30120-LOC_Os12g30130 intergenic_region ; MODIFIER silent_mutation Average:38.792; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218054911 NA 2.11E-06 mr1010 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
vg1218054911 NA 2.41E-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
vg1218054911 NA 4.23E-06 mr1171 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
vg1218054911 NA 3.71E-12 mr1205 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
vg1218054911 NA 4.68E-08 mr1206 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
vg1218054911 NA 9.24E-06 mr1284 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
vg1218054911 NA 5.53E-07 mr1315 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
vg1218054911 NA 9.49E-07 mr1405 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
vg1218054911 6.69E-06 6.80E-09 mr1418 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
vg1218054911 2.09E-06 9.95E-10 mr1420 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
vg1218054911 NA 8.79E-09 mr1488 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
vg1218054911 6.48E-06 4.33E-08 mr1492 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
vg1218054911 NA 1.04E-09 mr1506 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
vg1218054911 NA 3.01E-07 mr1507 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
vg1218054911 NA 3.08E-06 mr1548 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
vg1218054911 NA 1.03E-06 mr1556 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
vg1218054911 NA 1.67E-07 mr1604 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
vg1218054911 NA 6.17E-08 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
vg1218054911 NA 1.19E-06 mr1646 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
vg1218054911 3.90E-06 2.96E-09 mr1764 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
vg1218054911 NA 6.86E-12 mr1775 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
vg1218054911 NA 3.92E-09 mr1779 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
vg1218054911 3.00E-07 5.45E-12 mr1797 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
vg1218054911 3.00E-07 5.45E-12 mr1801 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
vg1218054911 NA 9.45E-07 mr1802 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
vg1218054911 NA 6.99E-09 mr1810 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
vg1218054911 NA 4.53E-07 mr1811 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
vg1218054911 NA 3.68E-06 mr1812 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
vg1218054911 NA 8.58E-07 mr1816 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
vg1218054911 NA 4.19E-06 mr1881 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
vg1218054911 NA 7.69E-07 mr1886 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
vg1218054911 5.62E-06 6.47E-09 mr1992 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