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Detailed information for vg0515959945:

Variant ID: vg0515959945 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 15959945
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGATTGGTATCATTATCTTCACTACCACCAATATTTTTGCCACCTCTGGTAGGCAATATTATCTCTATATTGGTCGTCTTGTCTCTATGCCAACTGC[G/A]
TCAGCTACCATCAATGGACAATTGTGATTACGACAGAAGGACAAGCTATATGCTCAGGGGCTTACTAGCTCAAACACAAGTATCATACCTTCAATTTGGA

Reverse complement sequence

TCCAAATTGAAGGTATGATACTTGTGTTTGAGCTAGTAAGCCCCTGAGCATATAGCTTGTCCTTCTGTCGTAATCACAATTGTCCATTGATGGTAGCTGA[C/T]
GCAGTTGGCATAGAGACAAGACGACCAATATAGAGATAATATTGCCTACCAGAGGTGGCAAAAATATTGGTGGTAGTGAAGATAATGATACCAATCAAAA

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 79.70% 18.50% 0.83% 0.97% NA
All Indica  2759 84.40% 13.20% 1.09% 1.38% NA
All Japonica  1512 72.60% 26.60% 0.40% 0.46% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 95.60% 2.70% 0.67% 1.01% NA
Indica II  465 74.40% 24.30% 0.86% 0.43% NA
Indica III  913 77.70% 19.50% 1.10% 1.75% NA
Indica Intermediate  786 89.60% 7.10% 1.53% 1.78% NA
Temperate Japonica  767 90.00% 10.00% 0.00% 0.00% NA
Tropical Japonica  504 58.90% 40.10% 0.40% 0.60% NA
Japonica Intermediate  241 45.60% 51.00% 1.66% 1.66% NA
VI/Aromatic  96 5.20% 93.80% 1.04% 0.00% NA
Intermediate  90 75.60% 21.10% 2.22% 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
vg0515959945 G -> DEL N N silent_mutation Average:31.13; most accessible tissue: Minghui63 flag leaf, score: 36.591 N N N N
vg0515959945 G -> A LOC_Os05g27450.1 downstream_gene_variant ; 1454.0bp to feature; MODIFIER silent_mutation Average:31.13; most accessible tissue: Minghui63 flag leaf, score: 36.591 N N N N
vg0515959945 G -> A LOC_Os05g27440-LOC_Os05g27450 intergenic_region ; MODIFIER silent_mutation Average:31.13; most accessible tissue: Minghui63 flag leaf, score: 36.591 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515959945 NA 6.59E-06 mr1117 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
vg0515959945 NA 8.03E-06 mr1496 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
vg0515959945 NA 2.03E-07 mr1113_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
vg0515959945 NA 2.36E-06 mr1114_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
vg0515959945 NA 9.41E-07 mr1117_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
vg0515959945 NA 8.59E-07 mr1118_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
vg0515959945 NA 8.93E-07 mr1119_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
vg0515959945 NA 8.81E-07 mr1240_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
vg0515959945 4.30E-06 4.30E-06 mr1293_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
vg0515959945 NA 2.26E-07 mr1496_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
vg0515959945 NA 3.90E-06 mr1519_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
vg0515959945 NA 7.10E-07 mr1861_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