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Detailed information for vg0621414627:

Variant ID: vg0621414627 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21414627
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ATCACAGAAGAATATGGAAACATTTATTCCCTCCTCATGCATGCCACTGAGGAGTTTTTGGAACCAATTAAAGATATTCCTTAGGAAAAAGGAAGATTTT[G/T]
GAACTAAAGCTAGCCATGCATACCTAGAAATCTTTAGAGTTTCCTTGTTCATGGAATATTTCTTGGCAAATGTGTATCTTGAGAAACTATAAAAAATTCA

Reverse complement sequence

TGAATTTTTTATAGTTTCTCAAGATACACATTTGCCAAGAAATATTCCATGAACAAGGAAACTCTAAAGATTTCTAGGTATGCATGGCTAGCTTTAGTTC[C/A]
AAAATCTTCCTTTTTCCTAAGGAATATCTTTAATTGGTTCCAAAAACTCCTCAGTGGCATGCATGAGGAGGGAATAAATGTTTCCATATTCTTCTGTGAT

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 98.30% 1.20% 0.49% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.70% 3.80% 1.52% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 96.30% 2.20% 1.43% 0.00% NA
Tropical Japonica  504 97.80% 1.80% 0.40% 0.00% NA
Japonica Intermediate  241 83.00% 12.90% 4.15% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0621414627 G -> T LOC_Os06g36470.1 downstream_gene_variant ; 4304.0bp to feature; MODIFIER silent_mutation Average:47.301; most accessible tissue: Zhenshan97 flower, score: 71.992 N N N N
vg0621414627 G -> T LOC_Os06g36480.1 intron_variant ; MODIFIER silent_mutation Average:47.301; most accessible tissue: Zhenshan97 flower, score: 71.992 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621414627 NA 4.22E-07 mr1240 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
vg0621414627 7.77E-07 NA mr1549 Jap_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
vg0621414627 3.22E-08 1.12E-07 mr1550 Jap_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
vg0621414627 1.16E-06 6.15E-07 mr1745 Jap_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
vg0621414627 2.08E-07 3.77E-08 mr1757 Jap_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
vg0621414627 NA 5.19E-06 mr1917 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