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Detailed information for vg0520296341:

Variant ID: vg0520296341 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 20296341
Reference Allele: CAlternative Allele: CGGCGGTCTGACCGAAGTATATGT,CGGTGGTCTGACCGAAGTATATGT
Primary Allele: CSecondary Allele: CGGCGGTCTGACCGAAGTAT ATGT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGGGGGGTGAATGGTTGGTATGCCCAAAAACCAAAACATTTAGCGGAAATAAAAGTTACCCTCAAATTTAACGGATCGCGGTCTGACCGAAGTGTATG[C/CGGCGGTCTGACCGAAGTATATGT,CGGTGGTCTGACCGAAGTATATGT]
GCCGGTTTGACCGCCTGATGAACGTCGATCTGACCGAGATCGAACTCCGGTCGAACCACCGAGATCGCCTGCCACTCTCTGTTGCCGCCGCCGGTCTAAC

Reverse complement sequence

GTTAGACCGGCGGCGGCAACAGAGAGTGGCAGGCGATCTCGGTGGTTCGACCGGAGTTCGATCTCGGTCAGATCGACGTTCATCAGGCGGTCAAACCGGC[G/ACATATACTTCGGTCAGACCGCCG,ACATATACTTCGGTCAGACCACCG]
CATACACTTCGGTCAGACCGCGATCCGTTAAATTTGAGGGTAACTTTTATTTCCGCTAAATGTTTTGGTTTTTGGGCATACCAACCATTCACCCCCCCCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CGGCGGTCTGACCGAAGTAT ATGT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.20% 9.00% 0.80% 0.00% CGGTGGTCTGACCGAAGTATATGT: 0.04%
All Indica  2759 99.80% 0.10% 0.04% 0.00% NA
All Japonica  1512 70.40% 27.00% 2.45% 0.00% CGGTGGTCTGACCGAAGTATATGT: 0.13%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 98.70% 1.20% 0.13% 0.00% NA
Tropical Japonica  504 21.80% 71.80% 5.95% 0.00% CGGTGGTCTGACCGAAGTATATGT: 0.40%
Japonica Intermediate  241 82.20% 15.40% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0520296341 C -> CGGCGGTCTGACCGAAGTATATGT LOC_Os05g34280-LOC_Os05g34290 intergenic_region ; MODIFIER silent_mutation Average:42.113; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0520296341 C -> CGGTGGTCTGACCGAAGTATATGT LOC_Os05g34280-LOC_Os05g34290 intergenic_region ; MODIFIER silent_mutation Average:42.113; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0520296341 NA 1.73E-06 mr1518 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
vg0520296341 5.53E-06 9.39E-07 mr1676 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
vg0520296341 5.11E-09 2.46E-10 mr1676_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