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Detailed information for vg0918112167:

Variant ID: vg0918112167 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18112167
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, C: 0.04, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTCATTTGTGACAGTGTGAGATACCTTCACAGTGTTAGGATATGCTATGTAGTCCTATATTTGCAAATAACCAACAAGCAGAGAAACATTTTTTTCCCTC[C/A]
GAAAAATTGTGCCAAAACTCATGTATATCACTTATTTTTCCTTCCAAATGTGCTGTTTCTCACCAACATATGGAGAATTCTGAAATCAACTGCGCATAAC

Reverse complement sequence

GTTATGCGCAGTTGATTTCAGAATTCTCCATATGTTGGTGAGAAACAGCACATTTGGAAGGAAAAATAAGTGATATACATGAGTTTTGGCACAATTTTTC[G/T]
GAGGGAAAAAAATGTTTCTCTGCTTGTTGGTTATTTGCAAATATAGGACTACATAGCATATCCTAACACTGTGAAGGTATCTCACACTGTCACAAATGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.40% 35.60% 0.04% 0.00% NA
All Indica  2759 96.50% 3.40% 0.07% 0.00% NA
All Japonica  1512 0.50% 99.50% 0.00% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 92.90% 7.10% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 99.00% 0.90% 0.11% 0.00% NA
Indica Intermediate  786 96.30% 3.60% 0.13% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 0.60% 99.40% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg0918112167 C -> A LOC_Os09g29790.1 upstream_gene_variant ; 2854.0bp to feature; MODIFIER silent_mutation Average:52.172; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0918112167 C -> A LOC_Os09g29810.1 upstream_gene_variant ; 2958.0bp to feature; MODIFIER silent_mutation Average:52.172; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0918112167 C -> A LOC_Os09g29800.1 intron_variant ; MODIFIER silent_mutation Average:52.172; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918112167 NA 4.58E-10 mr1175 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
vg0918112167 NA 1.33E-07 mr1219 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
vg0918112167 NA 6.81E-07 mr1274 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
vg0918112167 NA 9.45E-09 mr1342 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
vg0918112167 NA 4.19E-20 mr1676 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
vg0918112167 NA 2.47E-06 mr1006_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
vg0918112167 NA 4.31E-12 mr1097_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
vg0918112167 NA 1.27E-06 mr1201_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
vg0918112167 NA 5.26E-10 mr1219_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
vg0918112167 NA 6.06E-07 mr1274_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
vg0918112167 NA 1.19E-11 mr1377_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
vg0918112167 NA 5.08E-20 mr1637_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
vg0918112167 NA 5.10E-09 mr1705_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