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Detailed information for vg0901739971:

Variant ID: vg0901739971 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 1739971
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TAAAACCACCTAATGTTGCCTAATTAACCAGCGAAGCATCTACCTAAATTCATACTAGTGGTACCAGGCATAGGGTACCCACTAGTTGGGGGTTTTGTTT[G/A]
TTCTAGGGTGAACAAGGTAATAATAACAATAGCAATAATAAGGTCATATAAAGATAAATAGGCATGGCTAAATAAAACAGTGATAACGCGGGAATTTAAA

Reverse complement sequence

TTTAAATTCCCGCGTTATCACTGTTTTATTTAGCCATGCCTATTTATCTTTATATGACCTTATTATTGCTATTGTTATTATTACCTTGTTCACCCTAGAA[C/T]
AAACAAAACCCCCAACTAGTGGGTACCCTATGCCTGGTACCACTAGTATGAATTTAGGTAGATGCTTCGCTGGTTAATTAGGCAACATTAGGTGGTTTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.10% 21.90% 0.02% 0.00% NA
All Indica  2759 98.20% 1.80% 0.00% 0.00% NA
All Japonica  1512 35.90% 64.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 3.10% 96.70% 0.13% 0.00% NA
Tropical Japonica  504 79.00% 21.00% 0.00% 0.00% NA
Japonica Intermediate  241 50.20% 49.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0901739971 G -> A LOC_Os09g03520.1 upstream_gene_variant ; 2655.0bp to feature; MODIFIER silent_mutation Average:34.784; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0901739971 G -> A LOC_Os09g03540.1 upstream_gene_variant ; 775.0bp to feature; MODIFIER silent_mutation Average:34.784; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0901739971 G -> A LOC_Os09g03530.1 downstream_gene_variant ; 199.0bp to feature; MODIFIER silent_mutation Average:34.784; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0901739971 G -> A LOC_Os09g03550.1 downstream_gene_variant ; 2016.0bp to feature; MODIFIER silent_mutation Average:34.784; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0901739971 G -> A LOC_Os09g03530-LOC_Os09g03540 intergenic_region ; MODIFIER silent_mutation Average:34.784; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0901739971 NA 5.03E-37 Grain_thickness 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
vg0901739971 NA 2.60E-14 Grain_thickness 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
vg0901739971 NA 4.09E-12 Grain_width 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
vg0901739971 NA 8.08E-06 mr1124 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
vg0901739971 4.25E-06 NA mr1150 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
vg0901739971 NA 4.87E-06 mr1211 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
vg0901739971 NA 9.88E-06 mr1295 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
vg0901739971 NA 6.15E-36 mr1486 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
vg0901739971 NA 6.10E-08 mr1552 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
vg0901739971 NA 4.98E-07 mr1629 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
vg0901739971 NA 3.95E-13 mr1879 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
vg0901739971 NA 5.92E-07 mr1551_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
vg0901739971 NA 1.91E-10 mr1552_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
vg0901739971 NA 1.08E-07 mr1578_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
vg0901739971 NA 3.63E-18 mr1980_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