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Detailed information for vg0314656096:

Variant ID: vg0314656096 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14656096
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTTGATAATATATTTGTTTTGTATATAAAAGATTACTATAATTTTTTTATAAACTTGATTAAACTAAAAAAATATTGGATTAGAAAAAAAAATCAAAC[G/A]
ACTTGTAATATTGGATTAGAAAATAAAATCAAAACGACGAGATACGAAATGGAGGGAGTACATTGTTTTCTAGAGCATTTTATAGAGCCTTTGCTCTTGG

Reverse complement sequence

CCAAGAGCAAAGGCTCTATAAAATGCTCTAGAAAACAATGTACTCCCTCCATTTCGTATCTCGTCGTTTTGATTTTATTTTCTAATCCAATATTACAAGT[C/T]
GTTTGATTTTTTTTTCTAATCCAATATTTTTTTAGTTTAATCAAGTTTATAAAAAAATTATAGTAATCTTTTATATACAAAACAAATATATTATCAAAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 5.60% 1.52% 0.00% NA
All Indica  2759 99.80% 0.00% 0.18% 0.00% NA
All Japonica  1512 78.30% 17.30% 4.43% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 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 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 60.10% 31.40% 8.47% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 5.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0314656096 G -> A LOC_Os03g25600.1 upstream_gene_variant ; 144.0bp to feature; MODIFIER silent_mutation Average:79.625; most accessible tissue: Minghui63 root, score: 91.896 N N N N
vg0314656096 G -> A LOC_Os03g25600.2 upstream_gene_variant ; 144.0bp to feature; MODIFIER silent_mutation Average:79.625; most accessible tissue: Minghui63 root, score: 91.896 N N N N
vg0314656096 G -> A LOC_Os03g25590-LOC_Os03g25600 intergenic_region ; MODIFIER silent_mutation Average:79.625; most accessible tissue: Minghui63 root, score: 91.896 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314656096 NA 5.71E-06 mr1026 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
vg0314656096 NA 9.79E-07 mr1069 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
vg0314656096 NA 5.29E-06 mr1072 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
vg0314656096 NA 8.89E-11 mr1137 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
vg0314656096 5.42E-06 1.16E-08 mr1164 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
vg0314656096 NA 2.77E-06 mr1202 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
vg0314656096 7.78E-07 2.66E-06 mr1210 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
vg0314656096 3.61E-06 8.11E-06 mr1305 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
vg0314656096 2.80E-06 2.80E-06 mr1430 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
vg0314656096 4.78E-06 4.78E-06 mr1476 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
vg0314656096 NA 7.78E-06 mr1492 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
vg0314656096 NA 3.97E-07 mr1521 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
vg0314656096 NA 4.16E-07 mr1576 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
vg0314656096 3.91E-07 8.68E-08 mr1585 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
vg0314656096 1.06E-06 4.13E-06 mr1586 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
vg0314656096 NA 5.17E-10 mr1617 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
vg0314656096 NA 4.28E-06 mr1937 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
vg0314656096 2.23E-06 2.23E-06 mr1955 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
vg0314656096 NA 9.14E-06 mr1959_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