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Detailed information for vg0506849316:

Variant ID: vg0506849316 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6849316
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCTTGTGTGATAGGAATATGAAACAGCTGGCCGATATAAGTAAATGCAATTACACATGGTTTTATAAAAGTAATGTGAAAACATGATTTTATACAGGT[C/T]
CGAGGACCATGGGCAGATCTTGCACAGCAGGGCTCTTCTCCGGTCATGCAACAAGACTCTTTAACCAATAATATAGAGAACAGATGGGTGCAGTAGATTT

Reverse complement sequence

AAATCTACTGCACCCATCTGTTCTCTATATTATTGGTTAAAGAGTCTTGTTGCATGACCGGAGAAGAGCCCTGCTGTGCAAGATCTGCCCATGGTCCTCG[G/A]
ACCTGTATAAAATCATGTTTTCACATTACTTTTATAAAACCATGTGTAATTGCATTTACTTATATCGGCCAGCTGTTTCATATTCCTATCACACAAGGAA

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 88.50% 11.40% 0.06% 0.00% NA
All Indica  2759 82.00% 17.90% 0.11% 0.00% NA
All Japonica  1512 97.40% 2.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 71.00% 29.00% 0.00% 0.00% NA
Indica III  913 74.40% 25.60% 0.00% 0.00% NA
Indica Intermediate  786 87.80% 11.80% 0.38% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 90.50% 9.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0506849316 C -> T LOC_Os05g11980.1 intron_variant ; MODIFIER silent_mutation Average:34.582; most accessible tissue: Callus, score: 70.096 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506849316 4.94E-62 9.14E-112 mr1039 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
vg0506849316 3.81E-56 6.66E-93 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
vg0506849316 6.59E-23 8.05E-39 mr1632 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
vg0506849316 2.78E-21 8.98E-30 mr1632 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
vg0506849316 4.51E-78 8.70E-121 mr1039_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
vg0506849316 2.54E-65 2.31E-99 mr1039_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
vg0506849316 1.53E-11 5.70E-18 mr1514_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
vg0506849316 1.53E-09 3.42E-10 mr1514_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
vg0506849316 1.94E-40 2.32E-61 mr1632_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
vg0506849316 1.82E-34 2.37E-49 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
vg0506849316 2.18E-09 NA mr1873_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
vg0506849316 2.96E-08 3.29E-10 mr1873_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