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Detailed information for vg1217551232:

Variant ID: vg1217551232 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17551232
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACACATCTATATTGCGTACCTATCAAATAAACAATTTAAGATCTATATTAACTGATTTATACGTACACTTAAACTGATGGACCCACTATTTAAATCATT[C/G]
GAACTATTTTTATTACATTGGACTATTATTCTCAAATAATGCATTCTTTCAAAATAAAGTCTACAACATTATATACTATATACTGTGTACCCATTAAATT

Reverse complement sequence

AATTTAATGGGTACACAGTATATAGTATATAATGTTGTAGACTTTATTTTGAAAGAATGCATTATTTGAGAATAATAGTCCAATGTAATAAAAATAGTTC[G/C]
AATGATTTAAATAGTGGGTCCATCAGTTTAAGTGTACGTATAAATCAGTTAATATAGATCTTAAATTGTTTATTTGATAGGTACGCAATATAGATGTGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.20% 14.60% 0.57% 14.62% NA
All Indica  2759 98.00% 0.70% 0.07% 1.20% NA
All Japonica  1512 16.10% 43.10% 1.06% 39.75% NA
Aus  269 95.50% 0.00% 1.86% 2.60% NA
Indica I  595 98.00% 0.30% 0.00% 1.68% NA
Indica II  465 97.40% 2.40% 0.00% 0.22% NA
Indica III  913 99.00% 0.30% 0.11% 0.55% NA
Indica Intermediate  786 97.30% 0.40% 0.13% 2.16% NA
Temperate Japonica  767 2.90% 76.40% 0.26% 20.47% NA
Tropical Japonica  504 28.40% 0.80% 2.78% 68.06% NA
Japonica Intermediate  241 32.40% 25.70% 0.00% 41.91% NA
VI/Aromatic  96 57.30% 0.00% 3.12% 39.58% NA
Intermediate  90 63.30% 22.20% 1.11% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217551232 C -> DEL N N silent_mutation Average:18.806; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1217551232 C -> G LOC_Os12g29510-LOC_Os12g29520 intergenic_region ; MODIFIER silent_mutation Average:18.806; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217551232 NA 1.11E-16 mr1116 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
vg1217551232 NA 1.19E-11 mr1198 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
vg1217551232 NA 2.86E-26 mr1223 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
vg1217551232 NA 9.26E-14 mr1239 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
vg1217551232 NA 3.31E-09 mr1275 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
vg1217551232 NA 1.76E-11 mr1307 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
vg1217551232 NA 1.52E-34 mr1350 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
vg1217551232 NA 6.12E-14 mr1376 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
vg1217551232 NA 6.12E-14 mr1431 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
vg1217551232 NA 9.09E-19 mr1529 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
vg1217551232 5.40E-06 4.47E-41 mr1601 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
vg1217551232 NA 1.34E-12 mr1636 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
vg1217551232 NA 5.58E-17 mr1653 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
vg1217551232 NA 1.20E-08 mr1659 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
vg1217551232 NA 1.37E-06 mr1681 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
vg1217551232 NA 3.62E-06 mr1819 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
vg1217551232 NA 2.75E-09 mr1866 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
vg1217551232 NA 3.96E-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
vg1217551232 NA 2.58E-33 mr1944 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
vg1217551232 NA 1.05E-32 mr1780_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