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Detailed information for vg0729253239:

Variant ID: vg0729253239 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 29253239
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGAGCTGACGTGTGGGTCCCACACTGGAGTGACGGCGATGGATGGAAAATGCGACGGCGGTGGCATGGATCCAATTTTACAAAGTTCCAGTGGCACTCA[G/A]
CAGATTTCGCAAATAGTACCGGCAATTTTCTAATATGGCAAAATTCTAGTGGCATGGATCCAATTAACCCTTTTTAAAACTCAATATATAAGCAATGTCA

Reverse complement sequence

TGACATTGCTTATATATTGAGTTTTAAAAAGGGTTAATTGGATCCATGCCACTAGAATTTTGCCATATTAGAAAATTGCCGGTACTATTTGCGAAATCTG[C/T]
TGAGTGCCACTGGAACTTTGTAAAATTGGATCCATGCCACCGCCGTCGCATTTTCCATCCATCGCCGTCACTCCAGTGTGGGACCCACACGTCAGCTCCA

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 97.00% 2.80% 0.21% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 90.90% 8.50% 0.60% 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 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 90.00% 9.10% 0.91% 0.00% NA
Tropical Japonica  504 94.40% 5.40% 0.20% 0.00% NA
Japonica Intermediate  241 86.70% 12.90% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0729253239 G -> A LOC_Os07g48880.1 upstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:60.308; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0729253239 G -> A LOC_Os07g48890.1 upstream_gene_variant ; 1207.0bp to feature; MODIFIER silent_mutation Average:60.308; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0729253239 G -> A LOC_Os07g48880.3 upstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:60.308; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0729253239 G -> A LOC_Os07g48880.4 upstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:60.308; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0729253239 G -> A LOC_Os07g48880.2 upstream_gene_variant ; 1269.0bp to feature; MODIFIER silent_mutation Average:60.308; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0729253239 G -> A LOC_Os07g48880-LOC_Os07g48890 intergenic_region ; MODIFIER silent_mutation Average:60.308; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729253239 8.33E-09 5.76E-09 mr1038_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
vg0729253239 1.87E-09 1.87E-09 mr1389_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
vg0729253239 NA 9.85E-06 mr1549_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
vg0729253239 NA 4.67E-06 mr1757_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