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Detailed information for vg0907387974:

Variant ID: vg0907387974 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7387974
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGTGATCAAGATGTAGTCAAGAGTTGGATCATGTTGTTGTAATTTCACTTTTTCTGTATTCTTTTCTTATTTAATTAATAAAATCTCTTAAACAGTGGG[G/A]
GCTTCCCCTGCTGTGTTCTTTAAAAAATATTCTTTTTATTTGATGAATATCAATAAAAAATTGTGAAGACTATACTCCTAGACAAAGTATAACTTTGGTA

Reverse complement sequence

TACCAAAGTTATACTTTGTCTAGGAGTATAGTCTTCACAATTTTTTATTGATATTCATCAAATAAAAAGAATATTTTTTAAAGAACACAGCAGGGGAAGC[C/T]
CCCACTGTTTAAGAGATTTTATTAATTAAATAAGAAAAGAATACAGAAAAAGTGAAATTACAACAACATGATCCAACTCTTGACTACATCTTGATCACTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 0.80% 0.95% 0.74% NA
All Indica  2759 99.20% 0.00% 0.00% 0.76% NA
All Japonica  1512 94.60% 2.40% 2.98% 0.00% NA
Aus  269 95.50% 0.00% 0.00% 4.46% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.20% 0.00% 0.00% 2.80% NA
Indica III  913 99.60% 0.00% 0.00% 0.44% NA
Indica Intermediate  786 99.50% 0.00% 0.00% 0.51% NA
Temperate Japonica  767 90.40% 4.00% 5.61% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 2.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0907387974 G -> DEL N N silent_mutation Average:34.041; most accessible tissue: Callus, score: 76.856 N N N N
vg0907387974 G -> A LOC_Os09g12840-LOC_Os09g12850 intergenic_region ; MODIFIER silent_mutation Average:34.041; most accessible tissue: Callus, score: 76.856 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907387974 NA 1.26E-10 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
vg0907387974 2.05E-06 2.35E-10 mr1757 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
vg0907387974 1.02E-07 3.65E-12 mr1549_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
vg0907387974 NA 1.93E-06 mr1550_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
vg0907387974 2.17E-08 1.52E-12 mr1757_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