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Detailed information for vg1208205606:

Variant ID: vg1208205606 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8205606
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TACTTTAACAGCAGATGAATATTACAACCTTATGGCCGATGAGAGGGAGGATCTAGTCTAGTCGCGATTGCGAGCTCTTGCAAAAGTTACCAAGGATAAG[A/G]
AGCGTGTTGCTCGGCATTACAATAAGAAAGTAGTACCCAAAGATTTTTCGGAGGGGGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAA

Reverse complement sequence

TTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCCCCCTCCGAAAAATCTTTGGGTACTACTTTCTTATTGTAATGCCGAGCAACACGCT[T/C]
CTTATCCTTGGTAACTTTTGCAAGAGCTCGCAATCGCGACTAGACTAGATCCTCCCTCTCATCGGCCATAAGGTTGTAATATTCATCTGCTGTTAAAGTA

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 60.70% 19.60% 5.56% 14.16% NA
All Indica  2759 89.50% 3.90% 6.09% 0.51% NA
All Japonica  1512 7.50% 48.60% 2.51% 41.40% NA
Aus  269 74.70% 14.10% 9.67% 1.49% NA
Indica I  595 83.70% 7.60% 8.07% 0.67% NA
Indica II  465 91.60% 4.70% 3.01% 0.65% NA
Indica III  913 92.60% 0.80% 6.02% 0.66% NA
Indica Intermediate  786 89.10% 4.30% 6.49% 0.13% NA
Temperate Japonica  767 8.00% 72.80% 1.69% 17.60% NA
Tropical Japonica  504 7.10% 18.30% 1.39% 73.21% NA
Japonica Intermediate  241 6.60% 35.30% 7.47% 50.62% NA
VI/Aromatic  96 42.70% 18.80% 28.12% 10.42% NA
Intermediate  90 48.90% 30.00% 4.44% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208205606 A -> DEL N N silent_mutation Average:33.952; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N
vg1208205606 A -> G LOC_Os12g14374.1 downstream_gene_variant ; 631.0bp to feature; MODIFIER silent_mutation Average:33.952; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N
vg1208205606 A -> G LOC_Os12g14390.1 downstream_gene_variant ; 748.0bp to feature; MODIFIER silent_mutation Average:33.952; most accessible tissue: Minghui63 flag leaf, score: 52.137 N N N N
vg1208205606 A -> G LOC_Os12g14374-LOC_Os12g14390 intergenic_region ; MODIFIER silent_mutation Average:33.952; 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
vg1208205606 NA 4.41E-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
vg1208205606 NA 5.44E-10 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
vg1208205606 3.52E-10 2.36E-15 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
vg1208205606 NA 3.99E-12 mr1002 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
vg1208205606 NA 1.40E-13 mr1013 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
vg1208205606 NA 4.57E-09 mr1013 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
vg1208205606 NA 7.84E-17 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
vg1208205606 NA 1.24E-10 mr1031 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
vg1208205606 NA 9.48E-08 mr1034 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
vg1208205606 NA 1.14E-16 mr1056 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
vg1208205606 NA 3.33E-09 mr1056 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
vg1208205606 8.86E-17 1.74E-23 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
vg1208205606 1.56E-08 3.78E-19 mr1002_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
vg1208205606 NA 1.49E-21 mr1010_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
vg1208205606 NA 2.57E-08 mr1010_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
vg1208205606 NA 3.01E-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
vg1208205606 NA 9.49E-09 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
vg1208205606 NA 7.10E-21 mr1013_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
vg1208205606 NA 8.05E-11 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
vg1208205606 NA 4.21E-20 mr1031_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
vg1208205606 NA 7.48E-13 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
vg1208205606 NA 1.49E-12 mr1182_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
vg1208205606 NA 3.27E-06 mr1211_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
vg1208205606 NA 6.09E-21 mr1361_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
vg1208205606 NA 5.65E-09 mr1361_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
vg1208205606 NA 2.76E-06 mr1554_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
vg1208205606 NA 3.83E-13 mr1853_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
vg1208205606 NA 6.46E-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
vg1208205606 NA 2.32E-11 mr1879_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
vg1208205606 NA 5.23E-06 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