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Detailed information for vg0312969719:

Variant ID: vg0312969719 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 12969719
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTCCTTCTTTCCTCCCAAAGTACGAAGAATGGTGTCTTAGGTAGGGATGGTAGATATTGGGTAGAAGTGAGTTTATATAGAGATGAAGGGGATTGGCT[A/T]
GCCGTTGTGGTCAATGGATCTACACGATAATGAGAGGCTGTTGCAAGTGGGCCTCCTTTGCTCTCAAGTAAGAATAATGACGTCTTAGGTGGAGATGGTA

Reverse complement sequence

TACCATCTCCACCTAAGACGTCATTATTCTTACTTGAGAGCAAAGGAGGCCCACTTGCAACAGCCTCTCATTATCGTGTAGATCCATTGACCACAACGGC[T/A]
AGCCAATCCCCTTCATCTCTATATAAACTCACTTCTACCCAATATCTACCATCCCTACCTAAGACACCATTCTTCGTACTTTGGGAGGAAAGAAGGACCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.00% 3.50% 0.44% 0.00% NA
All Indica  2759 99.70% 0.10% 0.14% 0.00% NA
All Japonica  1512 89.00% 10.10% 0.93% 0.00% NA
Aus  269 97.00% 2.60% 0.37% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 69.80% 27.60% 2.58% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 5.60% 2.22% 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
vg0312969719 A -> T LOC_Os03g22560.1 upstream_gene_variant ; 3699.0bp to feature; MODIFIER silent_mutation Average:49.53; most accessible tissue: Zhenshan97 young leaf, score: 68.794 N N N N
vg0312969719 A -> T LOC_Os03g22560-LOC_Os03g22570 intergenic_region ; MODIFIER silent_mutation Average:49.53; most accessible tissue: Zhenshan97 young leaf, score: 68.794 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0312969719 NA 3.49E-07 mr1136 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
vg0312969719 NA 1.46E-06 mr1188_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
vg0312969719 NA 1.11E-06 mr1218_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
vg0312969719 4.80E-06 4.80E-06 mr1333_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