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Detailed information for vg0601514136:

Variant ID: vg0601514136 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1514136
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGCCCGGTGAGCCAGAGCAGAGGCGAAAACGTCTTTGCTGTTACTGGTCCACCAGTGACAGCCGATGCCGCGCTCCCCACCAGCAGTGGCGCCGCGCCG[A/T]
GCGCGAACAGCCAGCCGAGCAGGCCCGCATGCTGGGAAGAGGTCACCGATGCCGGCGGGAGCGGCGCGAGGTGATGATGATGAGCCGGTGGGGTGCTGTG

Reverse complement sequence

CACAGCACCCCACCGGCTCATCATCATCACCTCGCGCCGCTCCCGCCGGCATCGGTGACCTCTTCCCAGCATGCGGGCCTGCTCGGCTGGCTGTTCGCGC[T/A]
CGGCGCGGCGCCACTGCTGGTGGGGAGCGCGGCATCGGCTGTCACTGGTGGACCAGTAACAGCAAAGACGTTTTCGCCTCTGCTCTGGCTCACCGGGCTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.60% 11.40% 0.00% 0.00% NA
All Indica  2759 80.70% 19.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 72.10% 27.90% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 76.50% 23.50% 0.00% 0.00% NA
Indica Intermediate  786 81.20% 18.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0601514136 A -> T LOC_Os06g03780.1 downstream_gene_variant ; 2014.0bp to feature; MODIFIER silent_mutation Average:77.302; most accessible tissue: Zhenshan97 young leaf, score: 85.886 N N N N
vg0601514136 A -> T LOC_Os06g03790.1 intron_variant ; MODIFIER silent_mutation Average:77.302; most accessible tissue: Zhenshan97 young leaf, score: 85.886 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601514136 6.65E-06 NA mr1336 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
vg0601514136 4.37E-06 2.26E-08 mr1336 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
vg0601514136 NA 1.55E-07 mr1739 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
vg0601514136 NA 2.17E-06 mr1740 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
vg0601514136 NA 6.06E-06 mr1319_2 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
vg0601514136 NA 4.85E-06 mr1438_2 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