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Detailed information for vg0918467471:

Variant ID: vg0918467471 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18467471
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGAACAACAAAAAGTGTATCTTCTGTTCAAATAATTCACCACACCAAATATCTCTTTCAGATTTTGTCTTTTCAGCCACAGTCTTATTTTACTGTATAA[T/C]
TATTTATAACCACTTCTTTTGAATACCCATTTTTGCTCTTGCAGGGAACATGGCAATTAGTTTTCATGGCACTCTGACTGGAAGGACTTTGAGCAATTTC

Reverse complement sequence

GAAATTGCTCAAAGTCCTTCCAGTCAGAGTGCCATGAAAACTAATTGCCATGTTCCCTGCAAGAGCAAAAATGGGTATTCAAAAGAAGTGGTTATAAATA[A/G]
TTATACAGTAAAATAAGACTGTGGCTGAAAAGACAAAATCTGAAAGAGATATTTGGTGTGGTGAATTATTTGAACAGAAGATACACTTTTTGTTGTTCTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 2.30% 1.16% 0.00% NA
All Indica  2759 94.20% 3.80% 1.99% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.50% 9.40% 6.05% 0.00% NA
Indica II  465 96.10% 2.80% 1.08% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 94.00% 4.50% 1.53% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 97.80% 2.20% 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
vg0918467471 T -> C LOC_Os09g30340.1 upstream_gene_variant ; 2231.0bp to feature; MODIFIER silent_mutation Average:47.424; most accessible tissue: Callus, score: 88.203 N N N N
vg0918467471 T -> C LOC_Os09g30350.1 downstream_gene_variant ; 2231.0bp to feature; MODIFIER silent_mutation Average:47.424; most accessible tissue: Callus, score: 88.203 N N N N
vg0918467471 T -> C LOC_Os09g30330.1 intron_variant ; MODIFIER silent_mutation Average:47.424; most accessible tissue: Callus, score: 88.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918467471 2.47E-07 2.28E-12 mr1138 Ind_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
vg0918467471 NA 1.95E-12 mr1707 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
vg0918467471 2.46E-08 2.73E-18 mr1728 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
vg0918467471 9.41E-06 1.62E-10 mr1860 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
vg0918467471 5.20E-06 3.58E-09 mr1138_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
vg0918467471 9.85E-10 1.52E-14 mr1707_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
vg0918467471 4.11E-13 1.12E-22 mr1728_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
vg0918467471 3.10E-06 1.00E-11 mr1860_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