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Detailed information for vg1207888547:

Variant ID: vg1207888547 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7888547
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, T: 0.23, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


TAAATCGCGAGACGAATCTTTTGAGCCTAATTAGGCCATGATTAGCCATAAGTGCTACAGTAACCCACATGTGCTAATGCCAGCTTAAGTAGGCTCAAAA[T/G]
ATTCGTCTCGCGGTTTCCAGGCGAGTTCTGAAATTAGTTTTTTCATTCGTGTCCGAAAACCCCTTCCGACATTCGGTCAAACGTCTGATGTGACACCTAA

Reverse complement sequence

TTAGGTGTCACATCAGACGTTTGACCGAATGTCGGAAGGGGTTTTCGGACACGAATGAAAAAACTAATTTCAGAACTCGCCTGGAAACCGCGAGACGAAT[A/C]
TTTTGAGCCTACTTAAGCTGGCATTAGCACATGTGGGTTACTGTAGCACTTATGGCTAATCATGGCCTAATTAGGCTCAAAAGATTCGTCTCGCGATTTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 18.90% 17.80% 0.53% 62.82% NA
All Indica  2759 2.90% 4.20% 0.65% 92.24% NA
All Japonica  1512 50.00% 45.20% 0.26% 4.56% NA
Aus  269 1.90% 1.90% 0.74% 95.54% NA
Indica I  595 3.00% 0.70% 1.51% 94.79% NA
Indica II  465 3.70% 1.70% 0.65% 93.98% NA
Indica III  913 1.20% 5.60% 0.11% 93.10% NA
Indica Intermediate  786 4.30% 6.70% 0.64% 88.30% NA
Temperate Japonica  767 70.80% 23.10% 0.52% 5.61% NA
Tropical Japonica  504 27.80% 68.30% 0.00% 3.97% NA
Japonica Intermediate  241 30.30% 67.20% 0.00% 2.49% NA
VI/Aromatic  96 22.90% 8.30% 1.04% 67.71% NA
Intermediate  90 32.20% 31.10% 0.00% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1207888547 T -> DEL N N silent_mutation Average:15.424; most accessible tissue: Callus, score: 74.87 N N N N
vg1207888547 T -> G LOC_Os12g13910.1 upstream_gene_variant ; 3828.0bp to feature; MODIFIER silent_mutation Average:15.424; most accessible tissue: Callus, score: 74.87 N N N N
vg1207888547 T -> G LOC_Os12g13900-LOC_Os12g13910 intergenic_region ; MODIFIER silent_mutation Average:15.424; most accessible tissue: Callus, score: 74.87 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207888547 NA 2.24E-10 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1207888547 NA 3.57E-11 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1207888547 2.50E-12 3.29E-18 mr1002 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
vg1207888547 3.28E-10 4.89E-19 mr1002 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
vg1207888547 NA 2.11E-12 mr1031 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
vg1207888547 NA 3.18E-06 mr1942 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
vg1207888547 1.07E-21 8.79E-29 mr1002_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
vg1207888547 3.01E-19 1.20E-32 mr1002_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
vg1207888547 NA 1.07E-12 mr1011_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
vg1207888547 NA 3.42E-08 mr1011_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
vg1207888547 NA 2.79E-07 mr1013_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
vg1207888547 NA 6.73E-08 mr1031_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
vg1207888547 NA 5.83E-06 mr1330_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
vg1207888547 NA 3.20E-06 mr1865_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
vg1207888547 NA 8.43E-07 mr1902_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