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Detailed information for vg0803181124:

Variant ID: vg0803181124 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 3181124
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACATATTATATAAGAAGGTGCCCGCGCATGTGCGCGGGCTATCTTTCTAGTTGAAACAAAAGTTGTTCAACCTGGCTAGGGTCAGGGATCACCGGTGTC[G/A]
TCGTATTCGTCTTCGATCGGGGGGCTGTATTCCGTACGCTTCACCTTGCAAACCACGTCGCCACTATTACTGTCCTTGTCGACGCCGGCGCCTTGGATTG

Reverse complement sequence

CAATCCAAGGCGCCGGCGTCGACAAGGACAGTAATAGTGGCGACGTGGTTTGCAAGGTGAAGCGTACGGAATACAGCCCCCCGATCGAAGACGAATACGA[C/T]
GACACCGGTGATCCCTGACCCTAGCCAGGTTGAACAACTTTTGTTTCAACTAGAAAGATAGCCCGCGCACATGCGCGGGCACCTTCTTATATAATATGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 6.20% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 80.90% 19.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 68.30% 31.70% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 82.60% 17.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0803181124 G -> A LOC_Os08g05910.1 downstream_gene_variant ; 1185.0bp to feature; MODIFIER silent_mutation Average:56.569; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0803181124 G -> A LOC_Os08g05910.2 downstream_gene_variant ; 1210.0bp to feature; MODIFIER silent_mutation Average:56.569; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0803181124 G -> A LOC_Os08g05900-LOC_Os08g05910 intergenic_region ; MODIFIER silent_mutation Average:56.569; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0803181124 NA 6.35E-08 Awn_length Jap_All Not 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
vg0803181124 2.33E-07 NA mr1062 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
vg0803181124 NA 3.13E-07 mr1062 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
vg0803181124 7.62E-06 2.48E-07 mr1343 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
vg0803181124 7.62E-07 9.66E-08 mr1456 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
vg0803181124 NA 4.26E-06 mr1531 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
vg0803181124 NA 5.87E-09 mr1624 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
vg0803181124 NA 2.60E-06 mr1815 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
vg0803181124 8.17E-06 NA mr1995 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
vg0803181124 NA 5.01E-07 mr1062_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
vg0803181124 NA 5.85E-06 mr1577_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
vg0803181124 NA 2.28E-07 mr1780_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