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Detailed information for vg0906684964:

Variant ID: vg0906684964 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6684964
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CTGAGAAGTCTAACCTAGCCAGAGTACGTGCCCCGACAAGGTCAGAACCATCGTCATCAACAGTTCGATCTCTCGAGATCGACCAAGCCTCTAGATACAC[G/A]
GCGTACCAAAAGATGTCAGACCGTATGATGTCAAACGAGTACGCAACAAGGTAATTGGTAGATTGGTTTTTTAAATTAATCTACTAATATCGTAGATACA

Reverse complement sequence

TGTATCTACGATATTAGTAGATTAATTTAAAAAACCAATCTACCAATTACCTTGTTGCGTACTCGTTTGACATCATACGGTCTGACATCTTTTGGTACGC[C/T]
GTGTATCTAGAGGCTTGGTCGATCTCGAGAGATCGAACTGTTGATGACGATGGTTCTGACCTTGTCGGGGCACGTACTCTGGCTAGGTTAGACTTCTCAG

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 96.70% 2.80% 0.55% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 90.10% 8.20% 1.65% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.10% 0.39% 0.00% NA
Tropical Japonica  504 72.60% 23.00% 4.37% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0906684964 G -> A LOC_Os09g11900.1 downstream_gene_variant ; 2881.0bp to feature; MODIFIER silent_mutation Average:40.132; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N
vg0906684964 G -> A LOC_Os09g11890-LOC_Os09g11900 intergenic_region ; MODIFIER silent_mutation Average:40.132; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906684964 NA 3.39E-06 mr1304 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
vg0906684964 NA 4.79E-06 mr1364 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
vg0906684964 NA 2.77E-06 mr1443 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
vg0906684964 1.32E-06 5.48E-10 mr1925 Jap_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
vg0906684964 1.25E-07 3.90E-10 mr1498_2 Jap_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