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Detailed information for vg0303633068:

Variant ID: vg0303633068 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 3633068
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTTCACGCTTTCGCATGAATTTTACCAGTAGAAGAAAGGTTGTTTGCTTTCGCAGTGAAGCCAATGTTGGTAGTAGTAATGGAGGTTGTGACCATACC[G/T]
ATGCCGAGGGTCAATCTGTCCAAAAGTCATCAATGAACTTCTGGTTAGTGAAGTGCTATCATAAAATTATGTTTGGATACAATGTTTTGAGAGTTCTGAA

Reverse complement sequence

TTCAGAACTCTCAAAACATTGTATCCAAACATAATTTTATGATAGCACTTCACTAACCAGAAGTTCATTGATGACTTTTGGACAGATTGACCCTCGGCAT[C/A]
GGTATGGTCACAACCTCCATTACTACTACCAACATTGGCTTCACTGCGAAAGCAAACAACCTTTCTTCTACTGGTAAAATTCATGCGAAAGCGTGAAACT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 8.40% 0.02% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 76.80% 23.10% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 73.10% 26.70% 0.13% 0.00% NA
Tropical Japonica  504 93.10% 6.90% 0.00% 0.00% NA
Japonica Intermediate  241 54.40% 45.60% 0.00% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0303633068 G -> T LOC_Os03g07110.1 synonymous_variant ; p.Arg215Arg; LOW synonymous_codon Average:59.516; most accessible tissue: Callus, score: 77.88 N N N N
vg0303633068 G -> T LOC_Os03g07110.2 synonymous_variant ; p.Arg215Arg; LOW synonymous_codon Average:59.516; most accessible tissue: Callus, score: 77.88 N N N N
vg0303633068 G -> T LOC_Os03g07110.3 synonymous_variant ; p.Arg215Arg; LOW synonymous_codon Average:59.516; most accessible tissue: Callus, score: 77.88 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0303633068 NA 4.49E-06 mr1180 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
vg0303633068 3.79E-08 NA mr1019_2 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
vg0303633068 4.41E-07 NA mr1027_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
vg0303633068 NA 6.34E-06 mr1027_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
vg0303633068 6.73E-06 NA mr1132_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
vg0303633068 NA 1.59E-06 mr1183_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