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Detailed information for vg0807974527:

Variant ID: vg0807974527 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7974527
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCTTCTAGTTTTCGTTGTACGTGTGTTCTCTTTCTTCCTTCACGTACGTTTCGAGTAAATGCTATCTCCTCGTCGTCTACTAAGGCCTAATTTAGTTCC[C/T]
AATTTTTTCTTCAAATTTTTAACTTCTCCATCACATCAAAACTTACCTACACACATAAACTTCCAACTTTTCCGTCACATCATTTCAATTTCAACCAAAC

Reverse complement sequence

GTTTGGTTGAAATTGAAATGATGTGACGGAAAAGTTGGAAGTTTATGTGTGTAGGTAAGTTTTGATGTGATGGAGAAGTTAAAAATTTGAAGAAAAAATT[G/A]
GGAACTAAATTAGGCCTTAGTAGACGACGAGGAGATAGCATTTACTCGAAACGTACGTGAAGGAAGAAAGAGAACACACGTACAACGAAAACTAGAAGGA

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 90.70% 7.80% 0.00% 1.48% NA
All Indica  2759 98.20% 1.70% 0.00% 0.04% NA
All Japonica  1512 87.70% 7.80% 0.00% 4.50% NA
Aus  269 53.20% 46.80% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 96.80% 3.20% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 1.90% 0.00% 0.13% NA
Temperate Japonica  767 90.60% 0.70% 0.00% 8.74% NA
Tropical Japonica  504 82.30% 17.70% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.00% 0.00% 0.41% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 0.00% 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
vg0807974527 C -> T LOC_Os08g13410.1 upstream_gene_variant ; 1816.0bp to feature; MODIFIER silent_mutation Average:50.764; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0807974527 C -> T LOC_Os08g13400.1 downstream_gene_variant ; 1352.0bp to feature; MODIFIER silent_mutation Average:50.764; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0807974527 C -> T LOC_Os08g13400-LOC_Os08g13410 intergenic_region ; MODIFIER silent_mutation Average:50.764; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0807974527 C -> DEL N N silent_mutation Average:50.764; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807974527 NA 1.13E-07 mr1057 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
vg0807974527 NA 3.24E-07 mr1262 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
vg0807974527 3.07E-06 NA mr1480 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
vg0807974527 NA 9.65E-07 mr1126_2 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
vg0807974527 NA 2.74E-09 mr1166_2 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
vg0807974527 NA 1.56E-06 mr1762_2 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