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Detailed information for vg0401117842:

Variant ID: vg0401117842 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1117842
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GCGGCGTAACCAGGCTAAGGTTGCTACGCCATCTGATTGCAGGCAAAGCTGAAGCTACTTATTTTGGCCTTGCCGATGTCTACTCAGGTGTGCAAATGCC[T/G]
AATGGAACATGGCAATCGCTGGACATAAATGTATTCACAGGCATTTCTGCAAGCAACAAGTTGGTGGAACAATTGGCTAAGTTAACACAGCTGAGATCGC

Reverse complement sequence

GCGATCTCAGCTGTGTTAACTTAGCCAATTGTTCCACCAACTTGTTGCTTGCAGAAATGCCTGTGAATACATTTATGTCCAGCGATTGCCATGTTCCATT[A/C]
GGCATTTGCACACCTGAGTAGACATCGGCAAGGCCAAAATAAGTAGCTTCAGCTTTGCCTGCAATCAGATGGCGTAGCAACCTTAGCCTGGTTACGCCGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.90% 29.40% 0.42% 0.32% NA
All Indica  2759 61.50% 37.90% 0.33% 0.29% NA
All Japonica  1512 87.70% 11.40% 0.66% 0.26% NA
Aus  269 67.30% 32.00% 0.37% 0.37% NA
Indica I  595 19.80% 79.70% 0.50% 0.00% NA
Indica II  465 79.10% 20.00% 0.43% 0.43% NA
Indica III  913 69.20% 30.20% 0.22% 0.33% NA
Indica Intermediate  786 73.70% 25.70% 0.25% 0.38% NA
Temperate Japonica  767 91.00% 7.80% 1.17% 0.00% NA
Tropical Japonica  504 87.50% 12.10% 0.00% 0.40% NA
Japonica Intermediate  241 77.60% 21.20% 0.41% 0.83% NA
VI/Aromatic  96 25.00% 74.00% 0.00% 1.04% NA
Intermediate  90 82.20% 16.70% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0401117842 T -> DEL LOC_Os04g02860.1 N frameshift_variant Average:63.593; most accessible tissue: Zhenshan97 flower, score: 76.324 N N N N
vg0401117842 T -> G LOC_Os04g02860.1 synonymous_variant ; p.Pro717Pro; LOW synonymous_codon Average:63.593; most accessible tissue: Zhenshan97 flower, score: 76.324 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401117842 2.53E-06 4.68E-15 mr1565 Ind_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
vg0401117842 NA 2.68E-06 mr1715 Ind_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
vg0401117842 NA 4.51E-06 mr1036_2 Ind_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
vg0401117842 NA 1.02E-07 mr1072_2 Ind_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
vg0401117842 NA 2.57E-07 mr1075_2 Ind_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
vg0401117842 NA 2.16E-06 mr1169_2 Ind_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
vg0401117842 NA 1.93E-08 mr1174_2 Ind_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
vg0401117842 NA 2.08E-08 mr1347_2 Ind_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
vg0401117842 NA 3.19E-06 mr1406_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
vg0401117842 NA 2.41E-07 mr1539_2 Ind_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
vg0401117842 NA 1.07E-08 mr1558_2 Ind_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
vg0401117842 2.44E-08 2.63E-11 mr1565_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
vg0401117842 2.27E-10 2.14E-21 mr1565_2 Ind_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
vg0401117842 NA 1.04E-06 mr1619_2 Ind_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
vg0401117842 NA 9.91E-07 mr1659_2 Ind_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
vg0401117842 NA 3.35E-10 mr1715_2 Ind_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
vg0401117842 NA 2.63E-06 mr1771_2 Ind_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
vg0401117842 7.89E-06 NA mr1788_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