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

Detailed information for vg0918591036:

Variant ID: vg0918591036 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18591036
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.35, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGCCATTTGTTAATCTCTGTTCATGTTCTACTTCATCTATTCAAACGATTATTTTCGCGAGTGTGAGGACTGAACTTTCCCTAACCAGCAATCTTCAC[T/C]
CGCGATCAAGCTAAGCTGGGCGCCGTAGCCAGCCGGCAGGGCCAAAGCCAGCTGCTACGGAAGAGCTAGCATAGGGGGCCCCAGGCGTCGACGGTACCCA

Reverse complement sequence

TGGGTACCGTCGACGCCTGGGGCCCCCTATGCTAGCTCTTCCGTAGCAGCTGGCTTTGGCCCTGCCGGCTGGCTACGGCGCCCAGCTTAGCTTGATCGCG[A/G]
GTGAAGATTGCTGGTTAGGGAAAGTTCAGTCCTCACACTCGCGAAAATAATCGTTTGAATAGATGAAGTAGAACATGAACAGAGATTAACAAATGGCAGG

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 45.80% 4.00% 35.80% 14.43% NA
All Indica  2759 9.20% 6.80% 59.33% 24.65% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 85.10% 0.00% 14.87% 0.00% NA
Indica I  595 7.10% 4.00% 49.92% 38.99% NA
Indica II  465 7.10% 3.20% 65.81% 23.87% NA
Indica III  913 4.50% 12.00% 66.48% 16.98% NA
Indica Intermediate  786 17.70% 4.80% 54.33% 23.16% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 81.10% 2.20% 14.44% 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
vg0918591036 T -> DEL N N silent_mutation Average:47.978; most accessible tissue: Minghui63 flag leaf, score: 57.881 N N N N
vg0918591036 T -> C LOC_Os09g30478-LOC_Os09g30486 intergenic_region ; MODIFIER silent_mutation Average:47.978; most accessible tissue: Minghui63 flag leaf, score: 57.881 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918591036 NA 5.42E-30 mr1208 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
vg0918591036 NA 9.48E-13 mr1233 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
vg0918591036 NA 1.26E-09 mr1342 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
vg0918591036 4.88E-08 NA mr1557 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
vg0918591036 NA 1.64E-08 mr1559 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
vg0918591036 3.71E-06 4.05E-22 mr1598 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
vg0918591036 NA 2.02E-38 mr1208_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
vg0918591036 NA 1.06E-24 mr1233_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
vg0918591036 NA 2.84E-06 mr1346_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
vg0918591036 2.25E-08 NA mr1557_2 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
vg0918591036 4.77E-06 NA mr1557_2 Ind_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
vg0918591036 NA 1.35E-06 mr1559_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
vg0918591036 1.20E-11 1.38E-43 mr1598_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
vg0918591036 9.63E-09 2.31E-09 mr1598_2 Ind_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
vg0918591036 NA 1.36E-24 mr1949_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
vg0918591036 NA 9.60E-09 mr1949_2 Ind_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