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Detailed information for vg0622673581:

Variant ID: vg0622673581 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22673581
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAGATAATAAACCAAGCTTGGCACATTAGTTCACCCTATTATCATGTAGAGTCTTCACTTACGGTGCTCTCTACTGGTAGTAGAAAGTAATATAAATC[G/A]
TTGATCTCATTTGATCGAAGGGTTCACATTTATTTATAATACCATCTTAGTTAGCGGCAATAGAAACGTGGAGGGGTATTATTGTCTGAAAAATAGGTGC

Reverse complement sequence

GCACCTATTTTTCAGACAATAATACCCCTCCACGTTTCTATTGCCGCTAACTAAGATGGTATTATAAATAAATGTGAACCCTTCGATCAAATGAGATCAA[C/T]
GATTTATATTACTTTCTACTACCAGTAGAGAGCACCGTAAGTGAAGACTCTACATGATAATAGGGTGAACTAATGTGCCAAGCTTGGTTTATTATCTTAA

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 89.30% 10.70% 0.04% 0.00% NA
All Indica  2759 99.20% 0.80% 0.07% 0.00% NA
All Japonica  1512 68.50% 31.50% 0.00% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.00% 0.80% 0.22% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 77.40% 22.60% 0.00% 0.00% NA
Tropical Japonica  504 63.10% 36.90% 0.00% 0.00% NA
Japonica Intermediate  241 51.50% 48.50% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0622673581 G -> A LOC_Os06g38310.1 intron_variant ; MODIFIER silent_mutation Average:46.772; most accessible tissue: Zhenshan97 flower, score: 71.382 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622673581 2.90E-06 NA mr1484 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
vg0622673581 4.16E-06 4.16E-06 mr1609 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
vg0622673581 NA 5.86E-07 mr1418_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
vg0622673581 NA 1.88E-06 mr1419_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
vg0622673581 NA 6.56E-06 mr1420_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
vg0622673581 NA 4.18E-07 mr1488_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
vg0622673581 NA 4.85E-06 mr1779_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
vg0622673581 NA 5.08E-07 mr1824_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