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Detailed information for vg0123827476:

Variant ID: vg0123827476 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23827476
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTCTCGCATCACATATTATATTTTTGAACCGTTTCCACCATAATGCTTTAAAAAAAGAGCTTTACAAAACTAGATCCGTCATCACTATATTTTGACAA[C/T]
GTTATAATATTGTTACTGCGAGAAAGTAACCCTGTTACTGCACGATGGTCGTCTTGTTACTACGCAATTCCTGCGAGACGAGGACAAAAAGAGGTGGACG

Reverse complement sequence

CGTCCACCTCTTTTTGTCCTCGTCTCGCAGGAATTGCGTAGTAACAAGACGACCATCGTGCAGTAACAGGGTTACTTTCTCGCAGTAACAATATTATAAC[G/A]
TTGTCAAAATATAGTGATGACGGATCTAGTTTTGTAAAGCTCTTTTTTTAAAGCATTATGGTGGAAACGGTTCAAAAATATAATATGTGATGCGAGAGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 4.30% 0.44% 0.61% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 83.80% 12.90% 1.39% 1.92% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 74.10% 23.90% 1.04% 1.04% NA
Tropical Japonica  504 96.60% 0.60% 0.79% 1.98% NA
Japonica Intermediate  241 88.00% 3.70% 3.73% 4.56% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0123827476 C -> T LOC_Os01g42024.1 upstream_gene_variant ; 2386.0bp to feature; MODIFIER silent_mutation Average:60.592; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg0123827476 C -> T LOC_Os01g42020.1 intron_variant ; MODIFIER silent_mutation Average:60.592; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg0123827476 C -> DEL N N silent_mutation Average:60.592; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123827476 NA 4.45E-06 mr1354 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
vg0123827476 7.57E-06 7.57E-06 mr1738 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