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Detailed information for vg0819055371:

Variant ID: vg0819055371 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19055371
Reference Allele: CAlternative Allele: A,T
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CAATATTTTTACTAACTATTTAACTGCAGGAAAGCGTACTATAAACCACTGAAAAAGGAAAGCATTATATGATGACTTATCTGAATTACAGAATATGTGG[C/A,T]
GTAGTTGTCCACTTACAAATGAATTCATCAACTAATTGATGAAAAATCCATCCAAAATACGAATTAGGACAAAATTGACCAGAATTAGCGGACATCGAGG

Reverse complement sequence

CCTCGATGTCCGCTAATTCTGGTCAATTTTGTCCTAATTCGTATTTTGGATGGATTTTTCATCAATTAGTTGATGAATTCATTTGTAAGTGGACAACTAC[G/T,A]
CCACATATTCTGTAATTCAGATAAGTCATCATATAATGCTTTCCTTTTTCAGTGGTTTATAGTACGCTTTCCTGCAGTTAAATAGTTAGTAAAAATATTG

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 96.20% 3.40% 0.34% 0.00% NA
All Indica  2759 98.90% 0.80% 0.25% 0.00% NA
All Japonica  1512 93.10% 6.90% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.90% 2.30% 0.77% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 90.10% 9.90% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 88.80% 11.20% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 38.50% 9.38% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0819055371 C -> T LOC_Os08g30870.1 downstream_gene_variant ; 1525.0bp to feature; MODIFIER N Average:34.86; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0819055371 C -> T LOC_Os08g30870-LOC_Os08g30900 intergenic_region ; MODIFIER N Average:34.86; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0819055371 C -> A LOC_Os08g30870.1 downstream_gene_variant ; 1525.0bp to feature; MODIFIER silent_mutation Average:34.86; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0819055371 C -> A LOC_Os08g30870-LOC_Os08g30900 intergenic_region ; MODIFIER silent_mutation Average:34.86; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819055371 2.92E-07 2.92E-07 mr1389 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
vg0819055371 2.09E-12 1.07E-10 mr1038_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
vg0819055371 1.03E-08 1.03E-08 mr1389_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