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Detailed information for vg0709269240:

Variant ID: vg0709269240 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9269240
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAATTGACGGTAGTGGCATGAGAGGGTGCGCAAATTTGGACCAATGGCATATAAGGGAAGAGCCAATTTTCAGTGGCATATAAGGGATCAAACCAATTTT[C/T]
AGTGGCATATAAGGGATTATCTCAAAAAAAAAATGCCCAAGGAGCTAGCTGTGGGTATGTGTTCGGGAACCCTCGCTCCCTTCCCTAGCTCGTGAAACAA

Reverse complement sequence

TTGTTTCACGAGCTAGGGAAGGGAGCGAGGGTTCCCGAACACATACCCACAGCTAGCTCCTTGGGCATTTTTTTTTTGAGATAATCCCTTATATGCCACT[G/A]
AAAATTGGTTTGATCCCTTATATGCCACTGAAAATTGGCTCTTCCCTTATATGCCATTGGTCCAAATTTGCGCACCCTCTCATGCCACTACCGTCAATTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 4.10% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 87.20% 12.80% 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  465 100.00% 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 82.50% 17.50% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.80% 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
vg0709269240 C -> T LOC_Os07g15950.1 upstream_gene_variant ; 2535.0bp to feature; MODIFIER silent_mutation Average:40.856; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0709269240 C -> T LOC_Os07g15950-LOC_Os07g15959 intergenic_region ; MODIFIER silent_mutation Average:40.856; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709269240 2.63E-06 1.85E-15 mr1549 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
vg0709269240 1.63E-06 1.37E-08 mr1550 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
vg0709269240 NA 6.87E-07 mr1723 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
vg0709269240 1.72E-07 1.27E-16 mr1757 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
vg0709269240 NA 2.28E-08 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
vg0709269240 NA 7.73E-07 mr1679_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
vg0709269240 NA 3.53E-06 mr1723_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
vg0709269240 NA 3.05E-09 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