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Detailed information for vg0135985488:

Variant ID: vg0135985488 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35985488
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTCCTCGACATCTTGAAGACGGACTCAAAGTTTTGGCAGTCTTTGGAAAATTGTCCTGTGGACATAAGACATAGTCAAAGATCGCAGTGGCGTTAGTC[G/A]
AGCATATCATAAATTATTTGGCAGGGAACTTGAAAGCATAAAAGGGAAAATTCAGATATATTGAAATTCAAAGAATTCGATTCGTTCTCCTCATATTGAA

Reverse complement sequence

TTCAATATGAGGAGAACGAATCGAATTCTTTGAATTTCAATATATCTGAATTTTCCCTTTTATGCTTTCAAGTTCCCTGCCAAATAATTTATGATATGCT[C/T]
GACTAACGCCACTGCGATCTTTGACTATGTCTTATGTCCACAGGACAATTTTCCAAAGACTGCCAAAACTTTGAGTCCGTCTTCAAGATGTCGAGGAAGA

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 87.70% 12.30% 0.00% 0.00% NA
All Indica  2759 79.00% 21.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 94.20% 5.80% 0.00% 0.00% NA
Indica III  913 62.10% 37.90% 0.00% 0.00% NA
Indica Intermediate  786 75.20% 24.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0135985488 G -> A LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:42.652; most accessible tissue: Callus, score: 65.033 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135985488 NA 3.18E-07 mr1078 Ind_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
vg0135985488 NA 9.50E-06 mr1131 Ind_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
vg0135985488 NA 3.43E-07 mr1213 Ind_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
vg0135985488 NA 2.62E-06 mr1887 Ind_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
vg0135985488 NA 9.66E-08 mr1200_2 Ind_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
vg0135985488 NA 6.64E-06 mr1364_2 Ind_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