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Detailed information for vg0611078070:

Variant ID: vg0611078070 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11078070
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATGGTGCGTACAAACTTTCATGGCAGAAAAGAGAAGACTTTCACCGTGTTCAGATCCAATTTTTTCTTCCGACTTTTTCCATCACATCAAATTTTCCT[A/C]
CTCACATAAACTTCCAACTTTTCGGTCACATCATTTCAATTTCAATCAAATTTTCAATTTTGGCATGAACTAAAAGCAGCCTTTGTATATGGATATTGCC

Reverse complement sequence

GGCAATATCCATATACAAAGGCTGCTTTTAGTTCATGCCAAAATTGAAAATTTGATTGAAATTGAAATGATGTGACCGAAAAGTTGGAAGTTTATGTGAG[T/G]
AGGAAAATTTGATGTGATGGAAAAAGTCGGAAGAAAAAATTGGATCTGAACACGGTGAAAGTCTTCTCTTTTCTGCCATGAAAGTTTGTACGCACCATAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.40% 0.90% 0.70% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.10% 2.70% 2.18% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 91.80% 4.40% 3.78% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 2.10% 1.66% 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
vg0611078070 A -> C LOC_Os06g19444.1 upstream_gene_variant ; 1349.0bp to feature; MODIFIER silent_mutation Average:55.201; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0611078070 A -> C LOC_Os06g19444.2 upstream_gene_variant ; 1349.0bp to feature; MODIFIER silent_mutation Average:55.201; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0611078070 A -> C LOC_Os06g19444-LOC_Os06g19460 intergenic_region ; MODIFIER silent_mutation Average:55.201; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611078070 NA 6.08E-11 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0611078070 NA 5.13E-06 mr1045 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
vg0611078070 NA 1.17E-06 mr1354 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
vg0611078070 2.25E-06 NA mr1310_2 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
vg0611078070 NA 3.04E-06 mr1354_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
vg0611078070 NA 2.54E-06 mr1549_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