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Detailed information for vg0810919840:

Variant ID: vg0810919840 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10919840
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAAAGGCAACTATCCATTGACAAACCAAACGGGAAGCATAGGAAGATAGAACTCCATAACTCGATAGGCACTTTATTGATACTCGGATTATTTCGTAAG[C/T,A]
AATCAAGATAAATATTATGAAAATTGTTGAAAAAATATGATATAACATCTGTAGCCCCCGTCTCACTAGTCAATGGCGAACCAGTTGATGTAGTGAGGCA

Reverse complement sequence

TGCCTCACTACATCAACTGGTTCGCCATTGACTAGTGAGACGGGGGCTACAGATGTTATATCATATTTTTTCAACAATTTTCATAATATTTATCTTGATT[G/A,T]
CTTACGAAATAATCCGAGTATCAATAAAGTGCCTATCGAGTTATGGAGTTCTATCTTCCTATGCTTCCCGTTTGGTTTGTCAATGGATAGTTGCCTTTGG

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 94.40% 5.40% 0.21% 0.00% NA
All Indica  2759 90.60% 9.00% 0.33% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 98.00% 1.80% 0.17% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 81.40% 18.00% 0.66% 0.00% NA
Indica Intermediate  786 92.70% 7.00% 0.25% 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 98.90% 0.00% 1.11% 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
vg0810919840 C -> T LOC_Os08g17800.1 downstream_gene_variant ; 755.0bp to feature; MODIFIER silent_mutation Average:39.465; most accessible tissue: Minghui63 flag leaf, score: 63.692 N N N N
vg0810919840 C -> T LOC_Os08g17810.1 downstream_gene_variant ; 207.0bp to feature; MODIFIER silent_mutation Average:39.465; most accessible tissue: Minghui63 flag leaf, score: 63.692 N N N N
vg0810919840 C -> T LOC_Os08g17800-LOC_Os08g17810 intergenic_region ; MODIFIER silent_mutation Average:39.465; most accessible tissue: Minghui63 flag leaf, score: 63.692 N N N N
vg0810919840 C -> A LOC_Os08g17800.1 downstream_gene_variant ; 755.0bp to feature; MODIFIER N Average:39.465; most accessible tissue: Minghui63 flag leaf, score: 63.692 N N N N
vg0810919840 C -> A LOC_Os08g17810.1 downstream_gene_variant ; 207.0bp to feature; MODIFIER N Average:39.465; most accessible tissue: Minghui63 flag leaf, score: 63.692 N N N N
vg0810919840 C -> A LOC_Os08g17800-LOC_Os08g17810 intergenic_region ; MODIFIER N Average:39.465; most accessible tissue: Minghui63 flag leaf, score: 63.692 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810919840 6.33E-06 NA mr1183 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
vg0810919840 1.15E-06 NA mr1503 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