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Detailed information for vg0905565379:

Variant ID: vg0905565379 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5565379
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGGAGATGGTGCAGCAGGAGGTGGCGGAGGAGCCGGAGGAGATGGTGCAGGAGGAGATGGCGGAGCCGGAGGAGATGGTGCACGAAATGCCGCTTGTC[G/A]
CCCAGGAAGAATGATGTACCACTTGCGCCATAGTATGATGGCGTGGCTTGTGTCTCGTAGATGCGTCTCACCGTCCCCTCCTGGGTAGTCCAACTCGAGG

Reverse complement sequence

CCTCGAGTTGGACTACCCAGGAGGGGACGGTGAGACGCATCTACGAGACACAAGCCACGCCATCATACTATGGCGCAAGTGGTACATCATTCTTCCTGGG[C/T]
GACAAGCGGCATTTCGTGCACCATCTCCTCCGGCTCCGCCATCTCCTCCTGCACCATCTCCTCCGGCTCCTCCGCCACCTCCTGCTGCACCATCTCCTTC

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 98.20% 1.10% 0.63% 0.00% NA
All Indica  2759 97.00% 1.90% 1.05% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 91.60% 4.90% 3.53% 0.00% NA
Indica II  465 98.50% 1.10% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 2.40% 0.76% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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
vg0905565379 G -> A LOC_Os09g10220.1 N stop_gained Average:35.546; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905565379 1.04E-06 1.04E-06 mr1335_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
vg0905565379 NA 7.39E-06 mr1359_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