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Detailed information for vg0414021996:

Variant ID: vg0414021996 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14021996
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CGGATTTGAGATATTTTTATAAAAACGGAACCTACATGATATGAGCAATCCATTTTTGAGATGATCCAATTTTAGTTTTGCACTTTGCGTTTGAGTCCCT[G/A]
TAATATTCATATTTACATTTGAGTCCTTATAATATTGATATTTACATTTGAGTCCCTGTTCGAGGTCAGTGGTCAGCTCTTGTTGAAAAAAAAAGTAAAA

Reverse complement sequence

TTTTACTTTTTTTTTCAACAAGAGCTGACCACTGACCTCGAACAGGGACTCAAATGTAAATATCAATATTATAAGGACTCAAATGTAAATATGAATATTA[C/T]
AGGGACTCAAACGCAAAGTGCAAAACTAAAATTGGATCATCTCAAAAATGGATTGCTCATATCATGTAGGTTCCGTTTTTATAAAAATATCTCAAATCCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.40% 23.70% 0.44% 3.47% NA
All Indica  2759 61.40% 34.70% 0.69% 3.19% NA
All Japonica  1512 94.30% 0.70% 0.07% 4.96% NA
Aus  269 53.20% 46.50% 0.37% 0.00% NA
Indica I  595 80.70% 17.10% 1.18% 1.01% NA
Indica II  465 48.80% 50.50% 0.43% 0.22% NA
Indica III  913 54.80% 38.60% 0.11% 6.57% NA
Indica Intermediate  786 62.10% 34.10% 1.15% 2.67% NA
Temperate Japonica  767 98.30% 0.10% 0.00% 1.56% NA
Tropical Japonica  504 98.40% 1.00% 0.00% 0.60% NA
Japonica Intermediate  241 73.00% 1.70% 0.41% 24.90% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 70.00% 28.90% 0.00% 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
vg0414021996 G -> DEL N N silent_mutation Average:34.029; most accessible tissue: Minghui63 flag leaf, score: 49.097 N N N N
vg0414021996 G -> A LOC_Os04g24440.1 upstream_gene_variant ; 3911.0bp to feature; MODIFIER silent_mutation Average:34.029; most accessible tissue: Minghui63 flag leaf, score: 49.097 N N N N
vg0414021996 G -> A LOC_Os04g24450.1 intron_variant ; MODIFIER silent_mutation Average:34.029; most accessible tissue: Minghui63 flag leaf, score: 49.097 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414021996 NA 8.47E-07 mr1403 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
vg0414021996 NA 1.22E-06 mr1608 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
vg0414021996 NA 2.64E-06 mr1818 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
vg0414021996 NA 1.78E-07 mr1830 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
vg0414021996 NA 4.15E-15 mr1846 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
vg0414021996 NA 9.14E-11 mr1846 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
vg0414021996 NA 7.95E-06 mr1062_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
vg0414021996 NA 1.94E-07 mr1304_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
vg0414021996 NA 6.84E-07 mr1608_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
vg0414021996 NA 8.48E-07 mr1608_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
vg0414021996 NA 3.05E-07 mr1696_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
vg0414021996 NA 3.04E-18 mr1830_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
vg0414021996 NA 3.26E-16 mr1830_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
vg0414021996 2.54E-07 2.41E-30 mr1846_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
vg0414021996 6.49E-08 2.69E-26 mr1846_2 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