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Detailed information for vg0235365192:

Variant ID: vg0235365192 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 35365192
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ATTATGAATCCTGTTCAAGTAGATGATCAGACCATTTCAGTACATTGAGGAGAAGCTCTGTGCAAGATATGGTTTAGCAGGACATTGTTTTTTTTTTATG[A/G]
TTTATGCAGGATTTTGTACTATCGTCAAGCTAAAACTTCTTTTATACTTAATTCCTACAGAAGCACTGTAATCTGAAGGACTGAAACTACTTTTAAAACT

Reverse complement sequence

AGTTTTAAAAGTAGTTTCAGTCCTTCAGATTACAGTGCTTCTGTAGGAATTAAGTATAAAAGAAGTTTTAGCTTGACGATAGTACAAAATCCTGCATAAA[T/C]
CATAAAAAAAAAACAATGTCCTGCTAAACCATATCTTGCACAGAGCTTCTCCTCAATGTACTGAAATGGTCTGATCATCTACTTGAACAGGATTCATAAT

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 97.20% 2.60% 0.15% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 92.40% 7.10% 0.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 78.60% 20.40% 0.99% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0235365192 A -> G LOC_Os02g57750.1 intron_variant ; MODIFIER silent_mutation Average:57.46; most accessible tissue: Zhenshan97 flower, score: 87.365 N N N N
vg0235365192 A -> G LOC_Os02g57750.2 intron_variant ; MODIFIER silent_mutation Average:57.46; most accessible tissue: Zhenshan97 flower, score: 87.365 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0235365192 4.85E-09 2.92E-11 mr1125 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
vg0235365192 1.14E-08 5.84E-15 mr1136 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
vg0235365192 2.55E-11 1.92E-14 mr1188 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
vg0235365192 7.34E-09 1.54E-11 mr1448 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
vg0235365192 NA 2.71E-07 mr1830 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
vg0235365192 3.87E-09 9.16E-14 mr1125_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
vg0235365192 8.43E-06 8.64E-11 mr1136_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
vg0235365192 4.07E-09 7.16E-16 mr1188_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
vg0235365192 2.91E-07 2.91E-07 mr1448_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