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Detailed information for vg0602991597:

Variant ID: vg0602991597 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 2991597
Reference Allele: GAlternative Allele: GATCCAAAC
Primary Allele: GSecondary Allele: GATCCAAAC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAGTTCAGCGCAAAGTTTGGATTTTGATTGAAATTGAAGATGATATGACTGAAAAATTGTGTGTGTATGACAGGTTGATGTGATGGAAAATGACTTAA[G/GATCCAAAC]
TTTAGATCCAAACACAGTCCTAGTTTGCCATTTCGTTTCAAATGTCAGACACGTGAAATGACAAAAAATGGGTTCATTAATTTGCCAGGATGATACATGA

Reverse complement sequence

TCATGTATCATCCTGGCAAATTAATGAACCCATTTTTTGTCATTTCACGTGTCTGACATTTGAAACGAAATGGCAAACTAGGACTGTGTTTGGATCTAAA[C/GTTTGGATC]
TTAAGTCATTTTCCATCACATCAACCTGTCATACACACACAATTTTTCAGTCATATCATCTTCAATTTCAATCAAAATCCAAACTTTGCGCTGAACTAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GATCCAAAC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.70% 0.10% 5.76% 2.39% NA
All Indica  2759 86.20% 0.00% 9.75% 4.06% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 84.00% 0.00% 14.45% 1.51% NA
Indica II  465 94.00% 0.00% 5.38% 0.65% NA
Indica III  913 81.40% 0.00% 10.19% 8.43% NA
Indica Intermediate  786 88.80% 0.00% 8.27% 2.93% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 1.04% 1.04% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg0602991597 G -> DEL N N silent_mutation Average:43.238; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0602991597 G -> GATCCAAAC LOC_Os06g06400.1 upstream_gene_variant ; 731.0bp to feature; MODIFIER silent_mutation Average:43.238; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0602991597 G -> GATCCAAAC LOC_Os06g06420.1 upstream_gene_variant ; 4169.0bp to feature; MODIFIER silent_mutation Average:43.238; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0602991597 G -> GATCCAAAC LOC_Os06g06410.1 downstream_gene_variant ; 448.0bp to feature; MODIFIER silent_mutation Average:43.238; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0602991597 G -> GATCCAAAC LOC_Os06g06410.2 downstream_gene_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:43.238; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0602991597 G -> GATCCAAAC LOC_Os06g06400-LOC_Os06g06410 intergenic_region ; MODIFIER silent_mutation Average:43.238; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602991597 9.55E-06 6.61E-06 mr1265 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
vg0602991597 NA 4.04E-06 mr1352 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
vg0602991597 3.99E-06 4.63E-06 mr1712 Ind_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
vg0602991597 7.08E-07 NA mr1719 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