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Detailed information for vg0408995582:

Variant ID: vg0408995582 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 8995582
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTGGTAAAGACTCAATGATTGGGTCTCTAAATAAAGAACAAGGACCACCTCATGTTCAGCCAGGAACATCCTCAGGTAACATATCTTATCAAGTGATG[C/G]
CGATTTAAATAACTTCAGCTTACTCGTCTAATGTCTTGGAAATACATCAGGAACACTAGGCGATGACGAAGAAACAATTCCTCGCATAAAGGCGGCTGAT

Reverse complement sequence

ATCAGCCGCCTTTATGCGAGGAATTGTTTCTTCGTCATCGCCTAGTGTTCCTGATGTATTTCCAAGACATTAGACGAGTAAGCTGAAGTTATTTAAATCG[G/C]
CATCACTTGATAAGATATGTTACCTGAGGATGTTCCTGGCTGAACATGAGGTGGTCCTTGTTCTTTATTTAGAGACCCAATCATTGAGTCTTTACCAGCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.10% 5.40% 10.64% 51.82% NA
All Indica  2759 8.70% 9.10% 7.10% 75.06% NA
All Japonica  1512 71.00% 0.00% 11.31% 17.72% NA
Aus  269 45.40% 0.00% 30.48% 24.16% NA
Indica I  595 6.60% 4.00% 2.86% 86.55% NA
Indica II  465 3.70% 27.70% 6.02% 62.58% NA
Indica III  913 9.90% 0.30% 9.20% 80.61% NA
Indica Intermediate  786 12.10% 12.10% 8.52% 67.30% NA
Temperate Japonica  767 99.30% 0.00% 0.00% 0.65% NA
Tropical Japonica  504 18.70% 0.00% 32.54% 48.81% NA
Japonica Intermediate  241 90.00% 0.00% 2.90% 7.05% NA
VI/Aromatic  96 39.60% 0.00% 42.71% 17.71% NA
Intermediate  90 48.90% 5.60% 14.44% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0408995582 C -> DEL N N silent_mutation Average:6.295; most accessible tissue: Zhenshan97 root, score: 12.891 N N N N
vg0408995582 C -> G LOC_Os04g16550.1 downstream_gene_variant ; 1518.0bp to feature; MODIFIER silent_mutation Average:6.295; most accessible tissue: Zhenshan97 root, score: 12.891 N N N N
vg0408995582 C -> G LOC_Os04g16540.1 intron_variant ; MODIFIER silent_mutation Average:6.295; most accessible tissue: Zhenshan97 root, score: 12.891 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0408995582 NA 2.89E-06 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
vg0408995582 NA 1.51E-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
vg0408995582 NA 1.09E-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
vg0408995582 NA 1.10E-13 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
vg0408995582 NA 5.53E-09 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
vg0408995582 NA 9.53E-08 mr1304_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
vg0408995582 NA 2.68E-06 mr1547_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
vg0408995582 NA 2.16E-17 mr1830_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
vg0408995582 NA 9.72E-15 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
vg0408995582 3.05E-08 8.32E-30 mr1846_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
vg0408995582 9.62E-09 1.25E-26 mr1846_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