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Detailed information for vg0816453653:

Variant ID: vg0816453653 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16453653
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


ACCATTCATTAAAACAACAGATATGCTCTTTGTTGATCTAGATATCCTGTTGACTCTTGTTTTCATGTCCAACCCTCGCTAAATTATCTTCAAAGTATGG[C/T]
GCAACTTCTGTCATATGATAGAGGATAGTAAAATGGGCCTGGCCATACTCGTCTTGATCTGATACAGTTCTTTTTCTGCCTAATGTGGCAATACCGGATA

Reverse complement sequence

TATCCGGTATTGCCACATTAGGCAGAAAAAGAACTGTATCAGATCAAGACGAGTATGGCCAGGCCCATTTTACTATCCTCTATCATATGACAGAAGTTGC[G/A]
CCATACTTTGAAGATAATTTAGCGAGGGTTGGACATGAAAACAAGAGTCAACAGGATATCTAGATCAACAAAGAGCATATCTGTTGTTTTAATGAATGGT

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 97.70% 1.90% 0.32% 0.00% NA
All Indica  2759 99.90% 0.00% 0.11% 0.00% NA
All Japonica  1512 93.80% 5.80% 0.40% 0.00% NA
Aus  269 98.50% 0.00% 1.49% 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 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 82.90% 16.50% 0.60% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0816453653 C -> T LOC_Os08g26950.1 downstream_gene_variant ; 804.0bp to feature; MODIFIER silent_mutation Average:48.413; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N
vg0816453653 C -> T LOC_Os08g26950-LOC_Os08g26960 intergenic_region ; MODIFIER silent_mutation Average:48.413; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816453653 NA 8.91E-07 mr1076 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
vg0816453653 8.68E-06 NA mr1301 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
vg0816453653 4.11E-06 NA mr1410 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
vg0816453653 2.59E-06 8.50E-07 mr1411 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
vg0816453653 NA 8.22E-06 mr1220_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
vg0816453653 1.49E-08 NA mr1301_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
vg0816453653 1.70E-06 NA mr1410_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
vg0816453653 2.77E-06 NA mr1993_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