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Detailed information for vg0722219723:

Variant ID: vg0722219723 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22219723
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTATGTTTCTCTTCGTACAAGTCATATTTTTTCTTTGATAAATGCTGAGACGAAAGGCAATGATAAATCCATGAAGTCACTAAGCTCATATCCTTTA[T/C]
AGTAGCTTATGGGTTTCTCCACATTTGAGATGTACACGTCACTCAAAATAGTTTAAAAGCTATATTTGTTCCTGTTAAATTTACATTTTAAGACCCACAT

Reverse complement sequence

ATGTGGGTCTTAAAATGTAAATTTAACAGGAACAAATATAGCTTTTAAACTATTTTGAGTGACGTGTACATCTCAAATGTGGAGAAACCCATAAGCTACT[A/G]
TAAAGGATATGAGCTTAGTGACTTCATGGATTTATCATTGCCTTTCGTCTCAGCATTTATCAAAGAAAAAATATGACTTGTACGAAGAGAAACATAAAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.80% 1.40% 0.78% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 93.40% 4.20% 2.45% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.20% 3.10% 3.65% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.40% 0.00% NA
Japonica Intermediate  241 81.70% 15.40% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0722219723 T -> C LOC_Os07g37090.1 downstream_gene_variant ; 2574.0bp to feature; MODIFIER silent_mutation Average:29.483; most accessible tissue: Callus, score: 74.736 N N N N
vg0722219723 T -> C LOC_Os07g37080-LOC_Os07g37090 intergenic_region ; MODIFIER silent_mutation Average:29.483; most accessible tissue: Callus, score: 74.736 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722219723 NA 5.30E-06 mr1298_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
vg0722219723 NA 8.92E-06 mr1318_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
vg0722219723 NA 3.12E-06 mr1545_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
vg0722219723 4.55E-06 4.55E-06 mr1574_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
vg0722219723 NA 4.26E-06 mr1731_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