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Detailed information for vg0622678034:

Variant ID: vg0622678034 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22678034
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAACGCATGCATACACAACTGAAGCCCATCACCCTGCTGACCTTGGTGGCATATGGTATACGCAAGTAGTTTCTTATTAAGTGGGGGACTGAATAGTTT[G/A]
GTCCGTGTACTTATATACATGCATTCTGCACGTACGTGTAGGGGGATCAATGAGGTCCCTGTAGCTCACTGTGTACATATGGCTGAGGCTGCCTGGGTGA

Reverse complement sequence

TCACCCAGGCAGCCTCAGCCATATGTACACAGTGAGCTACAGGGACCTCATTGATCCCCCTACACGTACGTGCAGAATGCATGTATATAAGTACACGGAC[C/T]
AAACTATTCAGTCCCCCACTTAATAAGAAACTACTTGCGTATACCATATGCCACCAAGGTCAGCAGGGTGATGGGCTTCAGTTGTGTATGCATGCGTTGA

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 80.90% 18.90% 0.17% 0.00% NA
All Indica  2759 99.10% 0.90% 0.04% 0.00% NA
All Japonica  1512 45.80% 53.90% 0.26% 0.00% NA
Aus  269 89.20% 10.00% 0.74% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 56.30% 43.40% 0.26% 0.00% NA
Tropical Japonica  504 41.90% 57.70% 0.40% 0.00% NA
Japonica Intermediate  241 20.70% 79.30% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 1.11% 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
vg0622678034 G -> A LOC_Os06g38310.1 downstream_gene_variant ; 3420.0bp to feature; MODIFIER silent_mutation Average:60.45; most accessible tissue: Callus, score: 93.365 N N N N
vg0622678034 G -> A LOC_Os06g38310-LOC_Os06g38320 intergenic_region ; MODIFIER silent_mutation Average:60.45; most accessible tissue: Callus, score: 93.365 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622678034 2.32E-06 NA mr1136 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
vg0622678034 1.28E-06 NA mr1182 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
vg0622678034 NA 1.12E-06 mr1182 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
vg0622678034 2.53E-06 NA mr1650 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
vg0622678034 NA 1.81E-06 mr1650 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
vg0622678034 NA 3.15E-06 mr1658 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
vg0622678034 NA 4.59E-09 mr1379_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
vg0622678034 NA 1.54E-07 mr1691_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
vg0622678034 NA 8.08E-09 mr1851_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