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Detailed information for vg1204623065:

Variant ID: vg1204623065 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4623065
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTTCGATGTTAACCATGTAAGCAGATTACTATATGTGCTACGAGATTACATGGAACTTACATATAGTATATAAACCTCGGTTTTGGAGTAGATTGAAAA[T/C]
TGTCCGATCCGTCTATTAATCAGATTAAAACGGATTTAGCTACACGTGTGGGACGGACGAAAAAAACGCCCGGAATCCTTACATATTTTTTAATTATTAG

Reverse complement sequence

CTAATAATTAAAAAATATGTAAGGATTCCGGGCGTTTTTTTCGTCCGTCCCACACGTGTAGCTAAATCCGTTTTAATCTGATTAATAGACGGATCGGACA[A/G]
TTTTCAATCTACTCCAAAACCGAGGTTTATATACTATATGTAAGTTCCATGTAATCTCGTAGCACATATAGTAATCTGCTTACATGGTTAACATCGAAAG

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 41.50% 9.20% 6.52% 42.74% NA
All Indica  2759 13.20% 5.00% 9.97% 71.84% NA
All Japonica  1512 87.60% 11.80% 0.13% 0.46% NA
Aus  269 43.50% 42.40% 10.04% 4.09% NA
Indica I  595 3.70% 10.90% 6.22% 79.16% NA
Indica II  465 9.90% 1.10% 9.25% 79.78% NA
Indica III  913 20.90% 1.90% 13.25% 63.96% NA
Indica Intermediate  786 13.50% 6.40% 9.41% 70.74% NA
Temperate Japonica  767 95.20% 4.20% 0.26% 0.39% NA
Tropical Japonica  504 91.50% 7.90% 0.00% 0.60% NA
Japonica Intermediate  241 55.60% 44.00% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 2.10% 1.04% 1.04% NA
Intermediate  90 71.10% 4.40% 3.33% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1204623065 T -> C LOC_Os12g08890-LOC_Os12g08900 intergenic_region ; MODIFIER silent_mutation Average:13.189; most accessible tissue: Callus, score: 82.81 N N N N
vg1204623065 T -> DEL N N silent_mutation Average:13.189; most accessible tissue: Callus, score: 82.81 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204623065 NA 5.72E-06 mr1123 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
vg1204623065 7.24E-07 NA mr1679 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
vg1204623065 1.45E-07 3.71E-10 mr1679 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
vg1204623065 1.35E-08 5.03E-11 mr1691 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
vg1204623065 2.68E-11 1.58E-16 mr1693 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
vg1204623065 2.45E-07 3.04E-09 mr1720 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
vg1204623065 NA 1.83E-06 mr1496_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
vg1204623065 NA 4.72E-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
vg1204623065 NA 2.59E-08 mr1691_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
vg1204623065 NA 3.16E-07 mr1720_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