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Detailed information for vg0907841289:

Variant ID: vg0907841289 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7841289
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTACTTTCTTGTTTGACGTCGGAGATTGACTCAGACAAACCCTTTAGGTGTCCGCACGAGGCTGATAAAGGAAGTCTAACGTTATCTCTGAACTTATC[G/A]
AGAACGGTCACGTGCGCTCGATAACAGTTCCTCCAAGGTCTGCGGTTGAGAATATGAACTCGTTTATTTGCATTGAAGTCGGGGGATACTGTCAGGGTTA

Reverse complement sequence

TAACCCTGACAGTATCCCCCGACTTCAATGCAAATAAACGAGTTCATATTCTCAACCGCAGACCTTGGAGGAACTGTTATCGAGCGCACGTGACCGTTCT[C/T]
GATAAGTTCAGAGATAACGTTAGACTTCCTTTATCAGCCTCGTGCGGACACCTAAAGGGTTTGTCTGAGTCAATCTCCGACGTCAAACAAGAAAGTACAA

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 59.60% 39.80% 0.51% 0.00% NA
All Indica  2759 70.50% 29.20% 0.29% 0.00% NA
All Japonica  1512 42.30% 56.80% 0.93% 0.00% NA
Aus  269 68.00% 32.00% 0.00% 0.00% NA
Indica I  595 87.20% 12.80% 0.00% 0.00% NA
Indica II  465 83.00% 17.00% 0.00% 0.00% NA
Indica III  913 54.40% 45.00% 0.55% 0.00% NA
Indica Intermediate  786 69.00% 30.70% 0.38% 0.00% NA
Temperate Japonica  767 75.40% 23.10% 1.56% 0.00% NA
Tropical Japonica  504 3.20% 96.40% 0.40% 0.00% NA
Japonica Intermediate  241 18.70% 81.30% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 53.30% 44.40% 2.22% 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
vg0907841289 G -> A LOC_Os09g13530.1 upstream_gene_variant ; 1845.0bp to feature; MODIFIER silent_mutation Average:43.591; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N
vg0907841289 G -> A LOC_Os09g13520.1 downstream_gene_variant ; 2319.0bp to feature; MODIFIER silent_mutation Average:43.591; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N
vg0907841289 G -> A LOC_Os09g13520-LOC_Os09g13530 intergenic_region ; MODIFIER silent_mutation Average:43.591; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907841289 2.79E-06 NA mr1210 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
vg0907841289 NA 2.69E-10 mr1486 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
vg0907841289 4.12E-08 NA mr1585 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
vg0907841289 4.94E-07 NA mr1586 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
vg0907841289 NA 2.74E-11 mr1864 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
vg0907841289 NA 1.91E-07 mr1502_2 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
vg0907841289 NA 1.70E-06 mr1680_2 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