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Detailed information for vg0527579554:

Variant ID: vg0527579554 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27579554
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


GGTCCGAGATATATATATCTCTCTCTAGGTATCTCAAATTAGTAGCTACTTACTAATTAGTCTTCCTAGTTAGATTATTTCTTTTCCTTTTCTTTAGTTT[C/T]
TTCTTCTTCTTCTTCCTTGTTTTTCCTTTTTTGGTTTCTTGAGAAGCTCTAAGATGAGGGGCTTCTTGGCTAGAGGCTTGGGGTTCTACCTGGTTTCAGA

Reverse complement sequence

TCTGAAACCAGGTAGAACCCCAAGCCTCTAGCCAAGAAGCCCCTCATCTTAGAGCTTCTCAAGAAACCAAAAAAGGAAAAACAAGGAAGAAGAAGAAGAA[G/A]
AAACTAAAGAAAAGGAAAAGAAATAATCTAACTAGGAAGACTAATTAGTAAGTAGCTACTAATTTGAGATACCTAGAGAGAGATATATATATCTCGGACC

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 99.80% 0.20% 0.02% 0.00% NA
All Indica  2759 99.70% 0.20% 0.04% 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 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0527579554 C -> T LOC_Os05g48110.1 downstream_gene_variant ; 2787.0bp to feature; MODIFIER N Average:50.689; most accessible tissue: Callus, score: 83.572 N N N N
vg0527579554 C -> T LOC_Os05g48110-LOC_Os05g48120 intergenic_region ; MODIFIER N Average:50.689; most accessible tissue: Callus, score: 83.572 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527579554 NA 1.45E-06 mr1031 Jap_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
vg0527579554 NA 1.55E-06 mr1056 Jap_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
vg0527579554 NA 1.40E-06 mr1471 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
vg0527579554 NA 1.61E-07 mr1543 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
vg0527579554 NA 2.62E-06 mr1642 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
vg0527579554 NA 8.38E-07 mr1742 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
vg0527579554 NA 4.31E-07 mr1817 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
vg0527579554 NA 1.40E-06 mr1422_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
vg0527579554 NA 1.46E-16 mr1583_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
vg0527579554 NA 2.46E-09 mr1817_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
vg0527579554 NA 1.14E-12 mr1850_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