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Detailed information for vg0615048049:

Variant ID: vg0615048049 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15048049
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCAATCGGCTAAGGCAGACAAGAGTTTCTGTTCATCAAAGATTGGGTCCAGTAAATCAAGATCATGGCCAAGAGGACAATGTAATCAGGAAGAATCAAT[G/C]
GTGTCCTTCTAGTATTTTCACGAAGAATCAGAAGAGAAGGGTTCAGAGATTGAGGAACAGGGAGCACCTTCAGGAGGTTGAACAAGAAATTAATCATCGG

Reverse complement sequence

CCGATGATTAATTTCTTGTTCAACCTCCTGAAGGTGCTCCCTGTTCCTCAATCTCTGAACCCTTCTCTTCTGATTCTTCGTGAAAATACTAGAAGGACAC[C/G]
ATTGATTCTTCCTGATTACATTGTCCTCTTGGCCATGATCTTGATTTACTGGACCCAATCTTTGATGAACAGAAACTCTTGTCTGCCTTAGCCGATTGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.40% 32.30% 0.68% 0.68% NA
All Indica  2759 96.60% 3.20% 0.18% 0.04% NA
All Japonica  1512 8.90% 91.00% 0.07% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 93.90% 5.50% 0.50% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 94.40% 5.30% 0.13% 0.13% NA
Temperate Japonica  767 3.70% 96.30% 0.00% 0.00% NA
Tropical Japonica  504 17.70% 82.30% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.10% 0.41% 0.00% NA
VI/Aromatic  96 20.80% 22.90% 23.96% 32.29% NA
Intermediate  90 57.80% 38.90% 3.33% 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
vg0615048049 G -> C LOC_Os06g25760.1 missense_variant ; p.Trp531Ser; MODERATE nonsynonymous_codon ; W531S Average:25.243; most accessible tissue: Minghui63 panicle, score: 53.77 probably damaging 2.27 DELETERIOUS 0.00
vg0615048049 G -> DEL LOC_Os06g25760.1 N frameshift_variant Average:25.243; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615048049 NA 1.82E-23 mr1020 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
vg0615048049 NA 2.80E-06 mr1020 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
vg0615048049 NA 4.26E-19 mr1021 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
vg0615048049 NA 2.20E-16 mr1032 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
vg0615048049 3.22E-07 3.22E-07 mr1032 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
vg0615048049 NA 4.15E-12 mr1033 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
vg0615048049 NA 4.85E-18 mr1165 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
vg0615048049 NA 2.72E-20 mr1477 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
vg0615048049 NA 3.76E-17 mr1478 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
vg0615048049 1.17E-07 1.17E-07 mr1478 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
vg0615048049 4.79E-07 4.79E-07 mr1536 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
vg0615048049 NA 2.47E-22 mr1971 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
vg0615048049 NA 1.28E-07 mr1971 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
vg0615048049 NA 6.20E-16 mr1033_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
vg0615048049 NA 4.94E-09 mr1536_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