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Detailed information for vg0130973353:

Variant ID: vg0130973353 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30973353
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAAAAATAAGTATCATCTATTCCCTCCATCCTAAAATGTAACAACCTAATTAATACACACATCATAATACTAGAAAATGTGTCTAACTAGTACTAGGG[A/C]
CTTGTTTAGATTCAAACTTTTTTCTTCAAACTTCCAACTTTTCCGTCACATCAAATGTTTGGACACATGCATGGAGCATTAAATGTGGACGAAAAAAACC

Reverse complement sequence

GGTTTTTTTCGTCCACATTTAATGCTCCATGCATGTGTCCAAACATTTGATGTGACGGAAAAGTTGGAAGTTTGAAGAAAAAAGTTTGAATCTAAACAAG[T/G]
CCCTAGTACTAGTTAGACACATTTTCTAGTATTATGATGTGTGTATTAATTAGGTTGTTACATTTTAGGATGGAGGGAATAGATGATACTTATTTTTTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.40% 17.40% 2.20% 0.00% NA
All Indica  2759 98.50% 1.50% 0.04% 0.00% NA
All Japonica  1512 47.40% 46.00% 6.61% 0.00% NA
Aus  269 81.40% 18.60% 0.00% 0.00% NA
Indica I  595 97.00% 3.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.50% 0.13% 0.00% NA
Temperate Japonica  767 31.40% 58.90% 9.65% 0.00% NA
Tropical Japonica  504 77.40% 20.80% 1.79% 0.00% NA
Japonica Intermediate  241 35.30% 57.70% 7.05% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 77.80% 18.90% 3.33% 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
vg0130973353 A -> C LOC_Os01g53880.1 upstream_gene_variant ; 2412.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53880.2 upstream_gene_variant ; 2412.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53880.3 upstream_gene_variant ; 2412.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53880.4 upstream_gene_variant ; 2412.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53880.5 upstream_gene_variant ; 2412.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53880.6 upstream_gene_variant ; 2412.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53880.7 upstream_gene_variant ; 2412.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53870.1 downstream_gene_variant ; 3373.0bp to feature; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0130973353 A -> C LOC_Os01g53870-LOC_Os01g53880 intergenic_region ; MODIFIER silent_mutation Average:37.219; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130973353 NA 5.92E-11 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
vg0130973353 NA 2.32E-15 Plant_height 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
vg0130973353 NA 4.25E-15 Spikelet_length 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
vg0130973353 NA 2.80E-12 Spikelet_length 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
vg0130973353 1.52E-07 NA mr1070 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
vg0130973353 1.13E-07 4.41E-10 mr1070 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
vg0130973353 6.74E-06 NA mr1089 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
vg0130973353 1.78E-06 NA mr1092 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
vg0130973353 NA 8.42E-08 mr1092 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
vg0130973353 4.49E-07 NA mr1097 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
vg0130973353 NA 2.22E-08 mr1097 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
vg0130973353 4.91E-07 NA mr1128 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
vg0130973353 2.03E-08 2.03E-08 mr1128 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
vg0130973353 5.64E-06 NA mr1148 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
vg0130973353 6.32E-06 1.49E-07 mr1148 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
vg0130973353 6.73E-07 NA mr1154 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
vg0130973353 NA 4.81E-09 mr1154 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
vg0130973353 NA 7.59E-09 mr1252 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
vg0130973353 NA 8.89E-06 mr1872 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
vg0130973353 NA 1.22E-07 mr1896 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
vg0130973353 1.50E-07 NA mr1074_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
vg0130973353 1.82E-10 1.82E-10 mr1074_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
vg0130973353 3.86E-07 NA mr1089_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
vg0130973353 NA 1.46E-10 mr1089_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
vg0130973353 6.21E-10 NA mr1092_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
vg0130973353 2.55E-08 7.97E-12 mr1092_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
vg0130973353 1.69E-07 NA mr1097_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
vg0130973353 1.94E-07 2.96E-12 mr1097_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
vg0130973353 1.56E-07 NA mr1128_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
vg0130973353 3.12E-08 4.92E-10 mr1128_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
vg0130973353 7.05E-06 NA mr1129_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
vg0130973353 5.62E-06 6.51E-10 mr1129_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
vg0130973353 3.73E-06 NA mr1148_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
vg0130973353 7.06E-07 3.06E-09 mr1148_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
vg0130973353 1.02E-08 NA mr1152_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
vg0130973353 6.33E-07 2.81E-10 mr1152_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
vg0130973353 2.83E-08 NA mr1154_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
vg0130973353 1.17E-07 8.77E-12 mr1154_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
vg0130973353 NA 7.97E-06 mr1164_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
vg0130973353 7.13E-07 2.56E-08 mr1204_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
vg0130973353 8.77E-07 7.16E-10 mr1204_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
vg0130973353 3.21E-06 5.64E-10 mr1252_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
vg0130973353 NA 1.34E-08 mr1252_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
vg0130973353 NA 7.87E-07 mr1671_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
vg0130973353 NA 6.12E-10 mr1709_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
vg0130973353 NA 1.35E-09 mr1805_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
vg0130973353 NA 9.49E-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
vg0130973353 7.80E-08 7.80E-08 mr1889_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
vg0130973353 NA 1.21E-07 mr1896_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