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Detailed information for vg0904282939:

Variant ID: vg0904282939 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4282939
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACAACCTGGGAGATTTGCTTCACTCCAGTGCAGGTCTAAGGCTTGTCTCGAGTGTCAAGAGCGTGCCAGCTAGTTTGTTCTTACAACCAGCAAGAAAGA[C/T]
AAAGATCGGCTGATAGAGCCGATGACATATCGTCAGGACCTACCCGATACGGTTGAACCAAATCAGCTGTGGCTTTGAGATGAACACGTAAAACAAAACC

Reverse complement sequence

GGTTTTGTTTTACGTGTTCATCTCAAAGCCACAGCTGATTTGGTTCAACCGTATCGGGTAGGTCCTGACGATATGTCATCGGCTCTATCAGCCGATCTTT[G/A]
TCTTTCTTGCTGGTTGTAAGAACAAACTAGCTGGCACGCTCTTGACACTCGAGACAAGCCTTAGACCTGCACTGGAGTGAAGCAAATCTCCCAGGTTGTT

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 94.50% 5.50% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 84.00% 16.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 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 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 79.50% 20.50% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 71.00% 29.00% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0904282939 C -> T LOC_Os09g08290.1 downstream_gene_variant ; 3956.0bp to feature; MODIFIER silent_mutation Average:55.501; most accessible tissue: Zhenshan97 young leaf, score: 70.177 N N N N
vg0904282939 C -> T LOC_Os09g08280-LOC_Os09g08290 intergenic_region ; MODIFIER silent_mutation Average:55.501; most accessible tissue: Zhenshan97 young leaf, score: 70.177 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904282939 5.30E-08 NA Plant_height All YES 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
vg0904282939 NA 1.55E-12 Plant_height 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
vg0904282939 NA 8.63E-07 mr1380_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
vg0904282939 2.58E-06 2.58E-06 mr1908_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
vg0904282939 NA 4.67E-06 mr1996_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