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Detailed information for vg0724694719:

Variant ID: vg0724694719 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24694719
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

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:


TCATGGGCTGGTTCCGTTCGGGGCTAGTTCGGGGCGTGACAGCGTGACTGGCCGAGTGACAGACGAGACGGTGACAAGCCACGCGTTCTCTAGCCAGGTG[T/C]
CAGGCGGCGTGCGACAAATATGCCCTGTCATGTCAAGATGATGAGCGGCACAGTGCCTCATAACCATTCAGAGCCGGCTTGACCGCTCTGAACACACCGG

Reverse complement sequence

CCGGTGTGTTCAGAGCGGTCAAGCCGGCTCTGAATGGTTATGAGGCACTGTGCCGCTCATCATCTTGACATGACAGGGCATATTTGTCGCACGCCGCCTG[A/G]
CACCTGGCTAGAGAACGCGTGGCTTGTCACCGTCTCGTCTGTCACTCGGCCAGTCACGCTGTCACGCCCCGAACTAGCCCCGAACGGAACCAGCCCATGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.50% 30.00% 0.08% 0.36% NA
All Indica  2759 48.20% 51.10% 0.11% 0.58% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 29.60% 70.30% 0.17% 0.00% NA
Indica II  465 64.90% 33.80% 0.22% 1.08% NA
Indica III  913 50.70% 48.40% 0.11% 0.77% NA
Indica Intermediate  786 49.40% 50.10% 0.00% 0.51% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 10.00% 1.11% 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
vg0724694719 T -> DEL N N silent_mutation Average:62.51; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0724694719 T -> C LOC_Os07g41230.1 upstream_gene_variant ; 4776.0bp to feature; MODIFIER silent_mutation Average:62.51; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0724694719 T -> C LOC_Os07g41220-LOC_Os07g41230 intergenic_region ; MODIFIER silent_mutation Average:62.51; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724694719 NA 3.79E-07 Spikelet_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0724694719 NA 2.96E-08 mr1929 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
vg0724694719 NA 1.76E-06 mr1004_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
vg0724694719 NA 7.47E-08 mr1088_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
vg0724694719 1.90E-06 NA mr1224_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
vg0724694719 3.06E-06 2.45E-08 mr1224_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