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Detailed information for vg0919897205:

Variant ID: vg0919897205 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19897205
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.24, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TGTAGAAACGGCCCGTAAAACCGTCAGGACCGGGCGCCTTATCAGAGGGCAAGGACTTGATCACCGCCCAGACCTCATCCTCTGTGAAGGGACAGTCCAG[T/C]
CCCTCAAGCTGCGCAGGGCGGAGGCCAAGAGAGTGGAGGTCTAGGGCGAGTTCACGCTTGACGCTCGTCCCCAAGATGGCGCAAAAGTGAGAGGAGGCAA

Reverse complement sequence

TTGCCTCCTCTCACTTTTGCGCCATCTTGGGGACGAGCGTCAAGCGTGAACTCGCCCTAGACCTCCACTCTCTTGGCCTCCGCCCTGCGCAGCTTGAGGG[A/G]
CTGGACTGTCCCTTCACAGAGGATGAGGTCTGGGCGGTGATCAAGTCCTTGCCCTCTGATAAGGCGCCCGGTCCTGACGGTTTTACGGGCCGTTTCTACA

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 46.70% 40.30% 12.48% 0.49% NA
All Indica  2759 14.00% 66.60% 18.59% 0.80% NA
All Japonica  1512 99.50% 0.40% 0.13% 0.00% NA
Aus  269 62.80% 16.70% 20.45% 0.00% NA
Indica I  595 7.60% 70.60% 20.34% 1.51% NA
Indica II  465 15.90% 72.70% 10.54% 0.86% NA
Indica III  913 10.80% 68.60% 20.15% 0.44% NA
Indica Intermediate  786 21.50% 57.60% 20.23% 0.64% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.10% 0.41% 0.00% NA
VI/Aromatic  96 77.10% 5.20% 17.71% 0.00% NA
Intermediate  90 81.10% 14.40% 3.33% 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
vg0919897205 T -> DEL N N silent_mutation Average:37.152; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0919897205 T -> C LOC_Os09g33690.1 downstream_gene_variant ; 3299.0bp to feature; MODIFIER silent_mutation Average:37.152; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0919897205 T -> C LOC_Os09g33690.3 downstream_gene_variant ; 3299.0bp to feature; MODIFIER silent_mutation Average:37.152; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0919897205 T -> C LOC_Os09g33690.2 downstream_gene_variant ; 3299.0bp to feature; MODIFIER silent_mutation Average:37.152; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0919897205 T -> C LOC_Os09g33690.4 downstream_gene_variant ; 3299.0bp to feature; MODIFIER silent_mutation Average:37.152; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0919897205 T -> C LOC_Os09g33680-LOC_Os09g33690 intergenic_region ; MODIFIER silent_mutation Average:37.152; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919897205 NA 5.76E-07 mr1029 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
vg0919897205 NA 1.42E-10 mr1047 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
vg0919897205 NA 4.61E-10 mr1151 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
vg0919897205 NA 2.06E-16 mr1165 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
vg0919897205 NA 1.26E-11 mr1172 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
vg0919897205 NA 6.54E-07 mr1185 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
vg0919897205 NA 4.93E-07 mr1189 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
vg0919897205 4.55E-17 1.38E-14 mr1216 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
vg0919897205 1.19E-17 3.11E-30 mr1216 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
vg0919897205 NA 2.41E-09 mr1322 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
vg0919897205 NA 2.07E-06 mr1324 Ind_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
vg0919897205 NA 2.05E-12 mr1325 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
vg0919897205 NA 8.91E-15 mr1326 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
vg0919897205 NA 8.95E-06 mr1326 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
vg0919897205 NA 3.14E-14 mr1478 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
vg0919897205 NA 1.97E-06 mr1527 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
vg0919897205 NA 9.98E-08 mr1532 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
vg0919897205 NA 1.27E-06 mr1532 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
vg0919897205 NA 1.46E-06 mr1625 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
vg0919897205 NA 5.04E-08 mr1726 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
vg0919897205 NA 8.97E-15 mr1744 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
vg0919897205 NA 1.32E-31 mr1793 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
vg0919897205 NA 5.44E-09 mr1796 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
vg0919897205 NA 4.42E-09 mr1990 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
vg0919897205 NA 1.49E-07 mr1158_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
vg0919897205 NA 5.59E-06 mr1676_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
vg0919897205 6.10E-07 2.59E-49 mr1793_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