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Detailed information for vg0706116721:

Variant ID: vg0706116721 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 6116721
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCCTGCATTTTGAAATGGAGGGAGTATATGGTTAGCCCAAAAGTACAATTTTGGAATATATAATATTGACTAATACATAGTCCAAATAGAAATTACATC[A/G]
GTATTTCTTTTTGAAAACAGAAATTACATCAGTATATTGTCACTATGGCTGCGTTTAGATCCAGGGGTGTAAAGTTTTGGCGTGTCACATCGGATATGCT

Reverse complement sequence

AGCATATCCGATGTGACACGCCAAAACTTTACACCCCTGGATCTAAACGCAGCCATAGTGACAATATACTGATGTAATTTCTGTTTTCAAAAAGAAATAC[T/C]
GATGTAATTTCTATTTGGACTATGTATTAGTCAATATTATATATTCCAAAATTGTACTTTTGGGCTAACCATATACTCCCTCCATTTCAAAATGCAGGAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 2.20% 0.83% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 90.70% 6.90% 2.45% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 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 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 82.00% 13.60% 4.43% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0706116721 A -> G LOC_Os07g11060.1 upstream_gene_variant ; 1174.0bp to feature; MODIFIER silent_mutation Average:49.308; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0706116721 A -> G LOC_Os07g11060.2 upstream_gene_variant ; 1989.0bp to feature; MODIFIER silent_mutation Average:49.308; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0706116721 A -> G LOC_Os07g11070.1 downstream_gene_variant ; 1097.0bp to feature; MODIFIER silent_mutation Average:49.308; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0706116721 A -> G LOC_Os07g11060-LOC_Os07g11070 intergenic_region ; MODIFIER silent_mutation Average:49.308; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0706116721 NA 3.21E-06 Yield 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
vg0706116721 NA 3.13E-07 mr1585 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
vg0706116721 NA 9.17E-06 mr1836 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
vg0706116721 NA 5.00E-06 mr1161_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
vg0706116721 NA 1.58E-06 mr1793_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