Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0527589247:

Variant ID: vg0527589247 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589247
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.50, T: 0.50, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


CACGCGGAGATGCAGCGGTCGTCCCCTTCCTCTCGGTCGCAGGGGTCGGCGTCGGTGTTGCTCCAGGCAGCGATGCAGCGGCCATGCCCTTCCTCTCAGG[T/C]
GCAGGCGCCGGCGTTGCTCCAAGCGGCGATGCAGCCGCCGTCCTCTTCCTCGCAGGCGTCGGCGTCGGCGTTGTTCCAGGGGGCGCCCGCACGTCGACCA

Reverse complement sequence

TGGTCGACGTGCGGGCGCCCCCTGGAACAACGCCGACGCCGACGCCTGCGAGGAAGAGGACGGCGGCTGCATCGCCGCTTGGAGCAACGCCGGCGCCTGC[A/G]
CCTGAGAGGAAGGGCATGGCCGCTGCATCGCTGCCTGGAGCAACACCGACGCCGACCCCTGCGACCGAGAGGAAGGGGACGACCGCTGCATCTCCGCGTG

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 71.60% 25.60% 2.35% 0.47% NA
All Indica  2759 92.10% 3.30% 3.84% 0.80% NA
All Japonica  1512 29.50% 70.40% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 85.90% 0.50% 10.92% 2.69% NA
Indica II  465 84.70% 14.20% 1.08% 0.00% NA
Indica III  913 99.60% 0.00% 0.33% 0.11% NA
Indica Intermediate  786 92.40% 2.80% 4.20% 0.64% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 78.80% 21.00% 0.20% 0.00% NA
Japonica Intermediate  241 14.90% 84.60% 0.41% 0.00% NA
VI/Aromatic  96 66.70% 31.20% 2.08% 0.00% NA
Intermediate  90 71.10% 27.80% 1.11% 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
vg0527589247 T -> DEL LOC_Os05g48130.1 N frameshift_variant Average:28.405; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0527589247 T -> C LOC_Os05g48130.1 missense_variant ; p.Val31Ala; MODERATE nonsynonymous_codon ; V31A Average:28.405; most accessible tissue: Minghui63 panicle, score: 59.629 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527589247 NA 1.28E-33 mr1055 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
vg0527589247 NA 2.33E-06 mr1056 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
vg0527589247 NA 1.67E-51 mr1241 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
vg0527589247 NA 3.07E-06 mr1364 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
vg0527589247 NA 1.71E-06 mr1443 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
vg0527589247 NA 5.00E-11 mr1471 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
vg0527589247 NA 2.95E-06 mr1676 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
vg0527589247 NA 5.00E-07 mr1817 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
vg0527589247 NA 5.05E-64 mr1241_2 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
vg0527589247 NA 3.55E-09 mr1364_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
vg0527589247 NA 2.91E-06 mr1422_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