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Detailed information for vg0507977136:

Variant ID: vg0507977136 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7977136
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.31, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


CACAACTGCTAGCCAAGGCGGCTGTTGGGGCGGAGAAGGCCAGGGTGAAGAAGCTGGTGGCACCGGTCGCCAGTAAGCTCTACTAGAAAAACCATTTTTC[T/C]
TGATAATGGCATTTTTTTTCAGGCAGGTAGGCCTCTCGGAGCTAAATGACTGCTTGCTAAAGTGACAACCGCGGGGTGAGATGGTTGTCCGCATGCAAAA

Reverse complement sequence

TTTTGCATGCGGACAACCATCTCACCCCGCGGTTGTCACTTTAGCAAGCAGTCATTTAGCTCCGAGAGGCCTACCTGCCTGAAAAAAAATGCCATTATCA[A/G]
GAAAAATGGTTTTTCTAGTAGAGCTTACTGGCGACCGGTGCCACCAGCTTCTTCACCCTGGCCTTCTCCGCCCCAACAGCCGCCTTGGCTAGCAGTTGTG

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 56.00% 43.80% 0.21% 0.00% NA
All Indica  2759 83.40% 16.30% 0.29% 0.00% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 96.00% 3.50% 0.50% 0.00% NA
Indica II  465 68.20% 31.80% 0.00% 0.00% NA
Indica III  913 79.00% 20.80% 0.22% 0.00% NA
Indica Intermediate  786 88.20% 11.50% 0.38% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 53.30% 44.40% 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
vg0507977136 T -> C LOC_Os05g14220.1 upstream_gene_variant ; 1378.0bp to feature; MODIFIER silent_mutation Average:64.13; most accessible tissue: Minghui63 root, score: 77.29 N N N N
vg0507977136 T -> C LOC_Os05g14230.1 upstream_gene_variant ; 3804.0bp to feature; MODIFIER silent_mutation Average:64.13; most accessible tissue: Minghui63 root, score: 77.29 N N N N
vg0507977136 T -> C LOC_Os05g14220-LOC_Os05g14230 intergenic_region ; MODIFIER silent_mutation Average:64.13; most accessible tissue: Minghui63 root, score: 77.29 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507977136 3.87E-07 NA mr1039 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
vg0507977136 3.47E-06 4.45E-12 mr1039 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
vg0507977136 NA 2.25E-18 mr1133 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
vg0507977136 NA 3.57E-10 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
vg0507977136 NA 3.10E-10 mr1399 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
vg0507977136 NA 3.45E-07 mr1593 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
vg0507977136 NA 3.76E-13 mr1667 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
vg0507977136 NA 5.82E-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
vg0507977136 NA 1.64E-11 mr1039_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
vg0507977136 NA 6.83E-21 mr1195_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
vg0507977136 NA 4.67E-09 mr1593_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
vg0507977136 NA 5.26E-07 mr1632_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