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Detailed information for vg0108800483:

Variant ID: vg0108800483 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8800483
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTATACATATTTCCTTTAAAAATATATAGGTGTGTAAAGTAAATGTAGCGCGCGGGTCTTTTTTTTCTTCTCCAAATTGATTCCATCTTCGTATATCAA[C/T]
TATCGCATTACCATTGTTTCCAGATAGTGAAAGCAAATGTTATACTATCTCTCCAATTTTTTTTAATAGATAGGCTTTTAATATAATATTATTTGACCAT

Reverse complement sequence

ATGGTCAAATAATATTATATTAAAAGCCTATCTATTAAAAAAAATTGGAGAGATAGTATAACATTTGCTTTCACTATCTGGAAACAATGGTAATGCGATA[G/A]
TTGATATACGAAGATGGAATCAATTTGGAGAAGAAAAAAAAGACCCGCGCGCTACATTTACTTTACACACCTATATATTTTTAAAGGAAATATGTATACC

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 94.80% 2.30% 2.50% 0.38% NA
All Indica  2759 96.00% 0.30% 3.19% 0.54% NA
All Japonica  1512 91.50% 6.70% 1.65% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.30% 0.00% 5.21% 0.50% NA
Indica II  465 89.50% 0.40% 7.96% 2.15% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 0.60% 2.54% 0.25% NA
Temperate Japonica  767 97.10% 2.30% 0.39% 0.13% NA
Tropical Japonica  504 84.70% 11.70% 3.57% 0.00% NA
Japonica Intermediate  241 88.00% 10.40% 1.66% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 91.10% 2.20% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0108800483 C -> T LOC_Os01g15640.1 upstream_gene_variant ; 3120.0bp to feature; MODIFIER silent_mutation Average:42.659; most accessible tissue: Zhenshan97 root, score: 82.912 N N N N
vg0108800483 C -> T LOC_Os01g15640-LOC_Os01g15650 intergenic_region ; MODIFIER silent_mutation Average:42.659; most accessible tissue: Zhenshan97 root, score: 82.912 N N N N
vg0108800483 C -> DEL N N silent_mutation Average:42.659; most accessible tissue: Zhenshan97 root, score: 82.912 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0108800483 6.52E-06 6.52E-06 mr1085 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
vg0108800483 NA 7.05E-07 mr1104 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
vg0108800483 NA 5.13E-06 mr1155 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
vg0108800483 NA 3.62E-08 mr1213 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
vg0108800483 NA 5.46E-07 mr1224 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
vg0108800483 NA 2.56E-06 mr1225 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
vg0108800483 NA 2.97E-06 mr1104_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
vg0108800483 1.36E-07 7.84E-09 mr1224_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
vg0108800483 NA 2.84E-06 mr1246_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
vg0108800483 NA 1.61E-11 mr1410_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
vg0108800483 NA 3.29E-06 mr1620_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