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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0613547532:

Variant ID: vg0613547532 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 13547532
Reference Allele: TAlternative Allele: C,TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC,TCACTTATAAGCTAGCCATTGAAGTGAGGGGCTCCC
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAATAGCTTCCTCCTCTATGGAGGATACAAACGGTGTAGGATCGTAAAGGGTAAAGGGTCTTTCCCACCCCAAAAGCTAGCCATTGAGGTGAGGGGCTCC[T/C,TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC,TCACTTATAAGCTAGCCATTGAAGTGAGGGGCTCCC]
CCACTTATATCTTAGGTCCTTTGCCCTTCCTAGGGGTGGACAGGAAGCTCATGGCTCGTTAGCTCGCTCGGCTCGTGACAGGCTCGGCTCGGCTCGGCTC

Reverse complement sequence

GAGCCGAGCCGAGCCGAGCCTGTCACGAGCCGAGCGAGCTAACGAGCCATGAGCTTCCTGTCCACCCCTAGGAAGGGCAAAGGACCTAAGATATAAGTGG[A/G,GGGAGCCCCTCACCTCAATGGCTAGCTTATAA,GGGAGCCCCTCACTTCAATGGCTAGCTTATAAGTGA]
GGAGCCCCTCACCTCAATGGCTAGCTTTTGGGGTGGGAAAGACCCTTTACCCTTTACGATCCTACACCGTTTGTATCCTCCATAGAGGAGGAAGCTATTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.00% 37.40% 15.38% 0.00% TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC: 0.19%; TCACTTATAAGCTAGCCATTGAAGTGAGGGGCTCCC: 0.02%
All Indica  2759 64.60% 11.40% 23.74% 0.00% TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC: 0.29%; TCACTTATAAGCTAGCCATTGAAGTGAGGGGCTCCC: 0.04%
All Japonica  1512 7.00% 92.00% 0.99% 0.00% NA
Aus  269 77.00% 8.90% 14.13% 0.00% NA
Indica I  595 63.20% 7.60% 29.08% 0.00% TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC: 0.17%
Indica II  465 59.40% 11.40% 29.03% 0.00% TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC: 0.22%
Indica III  913 70.40% 10.30% 18.62% 0.00% TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC: 0.55%; TCACTTATAAGCTAGCCATTGAAGTGAGGGGCTCCC: 0.11%
Indica Intermediate  786 61.80% 15.50% 22.52% 0.00% TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC: 0.13%
Temperate Japonica  767 2.30% 96.30% 1.30% 0.00% NA
Tropical Japonica  504 14.10% 85.50% 0.40% 0.00% NA
Japonica Intermediate  241 7.10% 91.70% 1.24% 0.00% NA
VI/Aromatic  96 91.70% 4.20% 4.17% 0.00% NA
Intermediate  90 43.30% 38.90% 16.67% 0.00% TTATAAGCTAGCCATTGAGGTGAGGGGCTCCC: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0613547532 T -> C LOC_Os06g23190.1 downstream_gene_variant ; 2698.0bp to feature; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> C LOC_Os06g23200.1 downstream_gene_variant ; 1516.0bp to feature; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> C LOC_Os06g23190-LOC_Os06g23200 intergenic_region ; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> TTATAAGCTAGCCATTGAGGTGAGGGGCTC CC LOC_Os06g23190.1 downstream_gene_variant ; 2699.0bp to feature; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> TTATAAGCTAGCCATTGAGGTGAGGGGCTC CC LOC_Os06g23200.1 downstream_gene_variant ; 1515.0bp to feature; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> TTATAAGCTAGCCATTGAGGTGAGGGGCTC CC LOC_Os06g23190-LOC_Os06g23200 intergenic_region ; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> TCACTTATAAGCTAGCCATTGAAGTGAGGG GCTCCC LOC_Os06g23190.1 downstream_gene_variant ; 2699.0bp to feature; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> TCACTTATAAGCTAGCCATTGAAGTGAGGG GCTCCC LOC_Os06g23200.1 downstream_gene_variant ; 1515.0bp to feature; MODIFIER silent_mutation Average:36.219; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0613547532 T -> TCACTTATAAGCTAGCCATTGAAGTGAGGG GCTCCC LOC_Os06g23190-LOC_Os06g23200 intergenic_region ; MODIFIER silent_mutation Average:36.219; 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
vg0613547532 NA 2.80E-06 mr1020 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
vg0613547532 3.22E-07 3.22E-07 mr1032 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
vg0613547532 NA 1.02E-74 mr1033 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
vg0613547532 NA 4.25E-07 mr1033 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
vg0613547532 4.52E-06 4.15E-12 mr1033 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
vg0613547532 6.33E-06 6.33E-06 mr1165 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
vg0613547532 1.80E-07 1.26E-41 mr1176 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
vg0613547532 NA 7.59E-06 mr1176 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
vg0613547532 7.99E-06 5.97E-08 mr1176 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
vg0613547532 NA 3.01E-08 mr1301 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
vg0613547532 NA 4.06E-08 mr1410 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
vg0613547532 1.17E-07 1.17E-07 mr1478 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
vg0613547532 4.79E-07 4.79E-07 mr1536 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
vg0613547532 NA 2.46E-08 mr1806 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
vg0613547532 NA 1.28E-07 mr1971 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
vg0613547532 1.02E-12 1.12E-106 mr1033_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
vg0613547532 2.80E-07 6.55E-15 mr1033_2 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
vg0613547532 3.01E-07 6.20E-16 mr1033_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
vg0613547532 8.11E-06 NA mr1536_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
vg0613547532 6.67E-06 4.94E-09 mr1536_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
vg0613547532 NA 6.19E-07 mr1548_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