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Detailed information for vg1010660939:

Variant ID: vg1010660939 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10660939
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGACAAGCTATTACTTTCTCCTGAATCTTTTCTAGCTAACACATCGTTAGCAAGGGTGGGCGTGATGGAGTATGGATGGACCTGGATTTTGGTCTATG[C/T]
TGCTTCCGGATTTACCTAGGCACGAGCGAGGATTGCCCATCGCCTGTATAGGGATGGGGGTGAAAGTGGAGGTGGGTGTGTTGGTTAGGGGTGGTTATAT

Reverse complement sequence

ATATAACCACCCCTAACCAACACACCCACCTCCACTTTCACCCCCATCCCTATACAGGCGATGGGCAATCCTCGCTCGTGCCTAGGTAAATCCGGAAGCA[G/A]
CATAGACCAAAATCCAGGTCCATCCATACTCCATCACGCCCACCCTTGCTAACGATGTGTTAGCTAGAAAAGATTCAGGAGAAAGTAATAGCTTGTCAAG

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 96.10% 3.90% 0.00% 0.00% NA
All Indica  2759 93.50% 6.50% 0.00% 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 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 91.20% 8.80% 0.00% 0.00% NA
Indica Intermediate  786 92.20% 7.80% 0.00% 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 99.60% 0.40% 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
vg1010660939 C -> T LOC_Os10g21040.1 downstream_gene_variant ; 749.0bp to feature; MODIFIER silent_mutation Average:57.732; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg1010660939 C -> T LOC_Os10g21050.1 downstream_gene_variant ; 1486.0bp to feature; MODIFIER silent_mutation Average:57.732; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg1010660939 C -> T LOC_Os10g21060.1 downstream_gene_variant ; 3791.0bp to feature; MODIFIER silent_mutation Average:57.732; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg1010660939 C -> T LOC_Os10g21040-LOC_Os10g21050 intergenic_region ; MODIFIER silent_mutation Average:57.732; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010660939 1.14E-07 2.91E-11 Awn_length Ind_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1010660939 NA 4.22E-06 mr1672 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
vg1010660939 NA 8.71E-06 mr1925 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