Search for Variation information by Variation ID:

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

Detailed information for vg0728251275:

Variant ID: vg0728251275 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28251275
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.08, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCAAAGGAAGGGAGATAATTTAGTACAGTTGAGCCCACACATTCTTAAAAATAAAAGGATGAACCTACCCATGCAACAAGATTTTGCTCCCCTGCAGG[T/C]
TGGGTGTGATCAATGGCTTTACGTCCTGTAATGAGTTCAAGGAAGACAACGCCAAAGCTGTAAACATCAGATTTTACTGTCAACTGTCCTGTCATGGCAT

Reverse complement sequence

ATGCCATGACAGGACAGTTGACAGTAAAATCTGATGTTTACAGCTTTGGCGTTGTCTTCCTTGAACTCATTACAGGACGTAAAGCCATTGATCACACCCA[A/G]
CCTGCAGGGGAGCAAAATCTTGTTGCATGGGTAGGTTCATCCTTTTATTTTTAAGAATGTGTGGGCTCAACTGTACTAAATTATCTCCCTTCCTTTGGGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.90% 46.40% 0.21% 0.44% NA
All Indica  2759 43.60% 55.50% 0.33% 0.62% NA
All Japonica  1512 67.90% 31.90% 0.00% 0.13% NA
Aus  269 50.60% 49.40% 0.00% 0.00% NA
Indica I  595 58.70% 40.80% 0.17% 0.34% NA
Indica II  465 24.50% 74.40% 0.65% 0.43% NA
Indica III  913 47.50% 51.40% 0.22% 0.88% NA
Indica Intermediate  786 38.80% 60.20% 0.38% 0.64% NA
Temperate Japonica  767 96.20% 3.80% 0.00% 0.00% NA
Tropical Japonica  504 22.60% 77.20% 0.00% 0.20% NA
Japonica Intermediate  241 72.60% 27.00% 0.00% 0.41% NA
VI/Aromatic  96 78.10% 20.80% 1.04% 0.00% NA
Intermediate  90 66.70% 31.10% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728251275 T -> DEL LOC_Os07g47270.1 N frameshift_variant Average:55.702; most accessible tissue: Callus, score: 81.863 N N N N
vg0728251275 T -> C LOC_Os07g47270.1 synonymous_variant ; p.Gln286Gln; LOW synonymous_codon Average:55.702; most accessible tissue: Callus, score: 81.863 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728251275 NA 7.43E-06 mr1075 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
vg0728251275 NA 9.77E-06 mr1077 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
vg0728251275 NA 9.70E-07 mr1124 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
vg0728251275 NA 9.27E-07 mr1277 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
vg0728251275 NA 1.15E-07 mr1551 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
vg0728251275 NA 4.10E-14 mr1879 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
vg0728251275 NA 1.22E-09 mr1304_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
vg0728251275 NA 3.43E-08 mr1308_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
vg0728251275 NA 1.33E-09 mr1361_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
vg0728251275 NA 3.82E-13 mr1368_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
vg0728251275 NA 7.80E-06 mr1449_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
vg0728251275 NA 8.04E-16 mr1540_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
vg0728251275 NA 3.07E-07 mr1551_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
vg0728251275 NA 5.03E-11 mr1584_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
vg0728251275 NA 1.55E-06 mr1730_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
vg0728251275 NA 2.83E-15 mr1732_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
vg0728251275 NA 5.63E-06 mr1853_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
vg0728251275 NA 1.09E-06 mr1866_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
vg0728251275 NA 4.33E-11 mr1879_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
vg0728251275 NA 1.62E-10 mr1942_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