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Detailed information for vg0820065663:

Variant ID: vg0820065663 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20065663
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATCTTATTTGAAATTTTTTTATGATTACTATTTTTATTTTTATTAGATGATAAAACATGAATAGTATTTTTATATGTGATTCATTTTTTAAAAAATTTT[C/T]
ATAATTTTTTCAACTAAGACGAACGGTCAAACGCTGGATATGATATCCATGACTGCATTTATCTTGGGACGGAGGTAATTTCTTCGTTTCATATTATAAG

Reverse complement sequence

CTTATAATATGAAACGAAGAAATTACCTCCGTCCCAAGATAAATGCAGTCATGGATATCATATCCAGCGTTTGACCGTTCGTCTTAGTTGAAAAAATTAT[G/A]
AAAATTTTTTAAAAAATGAATCACATATAAAAATACTATTCATGTTTTATCATCTAATAAAAATAAAAATAGTAATCATAAAAAAATTTCAAATAAGATG

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 69.30% 30.20% 0.47% 0.00% NA
All Indica  2759 65.60% 33.80% 0.58% 0.00% NA
All Japonica  1512 89.40% 10.60% 0.00% 0.00% NA
Aus  269 4.50% 95.20% 0.37% 0.00% NA
Indica I  595 54.30% 45.40% 0.34% 0.00% NA
Indica II  465 88.60% 11.40% 0.00% 0.00% NA
Indica III  913 60.40% 38.80% 0.88% 0.00% NA
Indica Intermediate  786 66.80% 32.40% 0.76% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 74.80% 25.20% 0.00% 0.00% NA
Japonica Intermediate  241 88.00% 12.00% 0.00% 0.00% NA
VI/Aromatic  96 41.70% 53.10% 5.21% 0.00% NA
Intermediate  90 68.90% 31.10% 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
vg0820065663 C -> T LOC_Os08g32400.1 upstream_gene_variant ; 444.0bp to feature; MODIFIER silent_mutation Average:50.096; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0820065663 C -> T LOC_Os08g32390.1 downstream_gene_variant ; 3914.0bp to feature; MODIFIER silent_mutation Average:50.096; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0820065663 C -> T LOC_Os08g32390-LOC_Os08g32400 intergenic_region ; MODIFIER silent_mutation Average:50.096; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820065663 NA 4.77E-06 mr1445 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
vg0820065663 2.57E-06 2.57E-06 mr1601 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
vg0820065663 NA 1.08E-06 mr1830 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
vg0820065663 3.69E-06 NA mr1070_2 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
vg0820065663 7.22E-07 2.33E-06 mr1085_2 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
vg0820065663 2.69E-06 7.96E-07 mr1088_2 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
vg0820065663 2.98E-07 9.96E-08 mr1103_2 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
vg0820065663 5.01E-09 1.01E-10 mr1224_2 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
vg0820065663 8.88E-06 NA mr1226_2 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
vg0820065663 4.99E-07 4.99E-07 mr1233_2 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
vg0820065663 7.79E-07 NA mr1241_2 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
vg0820065663 NA 4.72E-06 mr1246_2 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
vg0820065663 2.72E-07 1.65E-09 mr1404_2 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
vg0820065663 1.19E-06 1.23E-06 mr1437_2 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
vg0820065663 2.18E-06 1.12E-08 mr1620_2 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
vg0820065663 1.42E-06 1.34E-06 mr1949_2 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