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Detailed information for vg1112908978:

Variant ID: vg1112908978 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 12908978
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TAAACCTCTGGTAAGCAAGCCTCATGAATTAACGACTCAACGACCCAATACTTCGTGACATGGGACCATCCAAACGGTCAACCGAACCGGCGAACGGAAC[C/T]
GACGGCTCAGACACGGTTTACGACAGAGACTCGGTACAGCAAGCGATAGGCCGGTAGGGGTTTAGGGATGCACCTATGGCTTTGCGACTCGGCTACTGAG

Reverse complement sequence

CTCAGTAGCCGAGTCGCAAAGCCATAGGTGCATCCCTAAACCCCTACCGGCCTATCGCTTGCTGTACCGAGTCTCTGTCGTAAACCGTGTCTGAGCCGTC[G/A]
GTTCCGTTCGCCGGTTCGGTTGACCGTTTGGATGGTCCCATGTCACGAAGTATTGGGTCGTTGAGTCGTTAATTCATGAGGCTTGCTTACCAGAGGTTTA

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 42.30% 31.40% 0.32% 26.03% NA
All Indica  2759 15.40% 41.60% 0.54% 42.48% NA
All Japonica  1512 95.50% 1.60% 0.00% 2.91% NA
Aus  269 0.00% 100.00% 0.00% 0.00% NA
Indica I  595 39.20% 19.20% 0.84% 40.84% NA
Indica II  465 9.70% 63.90% 0.65% 25.81% NA
Indica III  913 2.00% 41.20% 0.33% 56.52% NA
Indica Intermediate  786 16.30% 45.90% 0.51% 37.28% NA
Temperate Japonica  767 97.00% 2.10% 0.00% 0.91% NA
Tropical Japonica  504 92.30% 1.20% 0.00% 6.55% NA
Japonica Intermediate  241 97.50% 0.80% 0.00% 1.66% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 48.90% 35.60% 0.00% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1112908978 C -> T LOC_Os11g22460.1 upstream_gene_variant ; 1502.0bp to feature; MODIFIER silent_mutation Average:41.677; most accessible tissue: Zhenshan97 young leaf, score: 72.747 N N N N
vg1112908978 C -> T LOC_Os11g22449.1 downstream_gene_variant ; 3485.0bp to feature; MODIFIER silent_mutation Average:41.677; most accessible tissue: Zhenshan97 young leaf, score: 72.747 N N N N
vg1112908978 C -> T LOC_Os11g22460-LOC_Os11g22470 intergenic_region ; MODIFIER silent_mutation Average:41.677; most accessible tissue: Zhenshan97 young leaf, score: 72.747 N N N N
vg1112908978 C -> DEL N N silent_mutation Average:41.677; most accessible tissue: Zhenshan97 young leaf, score: 72.747 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1112908978 8.60E-06 NA mr1053 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
vg1112908978 2.47E-07 NA mr1067 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
vg1112908978 2.70E-07 NA mr1067 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
vg1112908978 NA 1.92E-06 mr1069 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
vg1112908978 NA 3.18E-06 mr1075 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
vg1112908978 4.02E-06 NA mr1077 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
vg1112908978 4.39E-06 8.33E-10 mr1077 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
vg1112908978 6.47E-07 NA mr1080 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
vg1112908978 NA 8.67E-07 mr1149 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
vg1112908978 NA 5.24E-06 mr1202 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
vg1112908978 NA 9.60E-06 mr1277 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
vg1112908978 NA 4.61E-09 mr1302 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
vg1112908978 NA 1.12E-06 mr1315 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
vg1112908978 8.09E-06 NA mr1411 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
vg1112908978 NA 2.99E-06 mr1418 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
vg1112908978 NA 1.28E-08 mr1420 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
vg1112908978 NA 1.41E-07 mr1424 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
vg1112908978 NA 1.03E-06 mr1646 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
vg1112908978 NA 1.38E-08 mr1659 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
vg1112908978 NA 1.63E-07 mr1764 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
vg1112908978 NA 8.06E-06 mr1771 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
vg1112908978 6.47E-08 NA mr1795 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
vg1112908978 2.36E-08 4.07E-08 mr1795 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
vg1112908978 NA 7.81E-07 mr1861 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
vg1112908978 NA 1.38E-06 mr1884 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
vg1112908978 NA 1.09E-11 mr1921 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
vg1112908978 NA 1.10E-06 mr1962 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