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Detailed information for vg1223868448:

Variant ID: vg1223868448 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23868448
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATCCAAACAATTGTTTTAAAGCATTCTTCTGTTTCTATTTTCCGGAAGAATTCGCAAGGCATGCATCTTAATTCTAAGTTTTTTATAACCCTGTGTTTT[A/T]
AAATTTTGGCGTTACAAAGGAGCCCTTAATTCTAAGAACGAAACAAGTGTTGAAATATAATATCAGTTTAAGCTTTTAAATGAGTGATTTGTTCACATAA

Reverse complement sequence

TTATGTGAACAAATCACTCATTTAAAAGCTTAAACTGATATTATATTTCAACACTTGTTTCGTTCTTAGAATTAAGGGCTCCTTTGTAACGCCAAAATTT[T/A]
AAAACACAGGGTTATAAAAAACTTAGAATTAAGATGCATGCCTTGCGAATTCTTCCGGAAAATAGAAACAGAAGAATGCTTTAAAACAATTGTTTGGATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.10% 32.80% 0.06% 0.00% NA
All Indica  2759 97.90% 2.10% 0.04% 0.00% NA
All Japonica  1512 9.70% 90.20% 0.07% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 98.00% 1.90% 0.11% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 4.40% 95.40% 0.13% 0.00% NA
Tropical Japonica  504 18.30% 81.70% 0.00% 0.00% NA
Japonica Intermediate  241 8.70% 91.30% 0.00% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 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
vg1223868448 A -> T LOC_Os12g38840.1 upstream_gene_variant ; 2002.0bp to feature; MODIFIER silent_mutation Average:30.579; most accessible tissue: Callus, score: 65.884 N N N N
vg1223868448 A -> T LOC_Os12g38840-LOC_Os12g38850 intergenic_region ; MODIFIER silent_mutation Average:30.579; most accessible tissue: Callus, score: 65.884 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223868448 NA 2.22E-11 mr1281 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
vg1223868448 NA 2.14E-20 mr1588 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
vg1223868448 3.15E-06 6.48E-40 mr1882 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
vg1223868448 NA 6.45E-16 mr1162_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
vg1223868448 NA 6.74E-22 mr1175_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
vg1223868448 NA 3.39E-09 mr1198_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
vg1223868448 NA 2.00E-25 mr1588_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
vg1223868448 NA 5.23E-06 mr1648_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
vg1223868448 NA 1.58E-18 mr1657_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