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Detailed information for vg0605662134:

Variant ID: vg0605662134 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5662134
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTATAGCTTGGTTAATCTTTTAGCGTGACTCCCTAGCGTGTTAACAGCCTATAGAAGTGGTGCAATTGAGGCCATATATGCTAGATTTTTTTTGTAATT[G/A,T]
GTGGTTTAATTGAGGCCATATAGTATATATGGGTTAATTATTTTACACGAAAAAATATGAATGGCTTGGTACTGTAAAATATCAACAATTAGTTGAAGCT

Reverse complement sequence

AGCTTCAACTAATTGTTGATATTTTACAGTACCAAGCCATTCATATTTTTTCGTGTAAAATAATTAACCCATATATACTATATGGCCTCAATTAAACCAC[C/T,A]
AATTACAAAAAAAATCTAGCATATATGGCCTCAATTGCACCACTTCTATAGGCTGTTAACACGCTAGGGAGTCACGCTAAAAGATTAACCAAGCTATAGA

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 72.40% 3.90% 6.56% 17.14% NA
All Indica  2759 63.20% 0.00% 10.15% 26.64% NA
All Japonica  1512 85.60% 12.10% 1.46% 0.86% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 47.20% 0.00% 23.36% 29.41% NA
Indica II  465 76.10% 0.00% 5.59% 18.28% NA
Indica III  913 63.40% 0.00% 5.48% 31.11% NA
Indica Intermediate  786 67.40% 0.00% 8.27% 24.30% NA
Temperate Japonica  767 78.10% 18.80% 2.35% 0.78% NA
Tropical Japonica  504 98.20% 1.40% 0.00% 0.40% NA
Japonica Intermediate  241 83.00% 13.30% 1.66% 2.07% NA
VI/Aromatic  96 38.50% 0.00% 6.25% 55.21% NA
Intermediate  90 88.90% 0.00% 1.11% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0605662134 G -> T LOC_Os06g10860.1 upstream_gene_variant ; 1834.0bp to feature; MODIFIER N Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> T LOC_Os06g10850.1 downstream_gene_variant ; 869.0bp to feature; MODIFIER N Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> T LOC_Os06g10870.1 downstream_gene_variant ; 3831.0bp to feature; MODIFIER N Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> T LOC_Os06g10850.2 downstream_gene_variant ; 869.0bp to feature; MODIFIER N Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> T LOC_Os06g10850-LOC_Os06g10860 intergenic_region ; MODIFIER N Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> A LOC_Os06g10860.1 upstream_gene_variant ; 1834.0bp to feature; MODIFIER silent_mutation Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> A LOC_Os06g10850.1 downstream_gene_variant ; 869.0bp to feature; MODIFIER silent_mutation Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> A LOC_Os06g10870.1 downstream_gene_variant ; 3831.0bp to feature; MODIFIER silent_mutation Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> A LOC_Os06g10850.2 downstream_gene_variant ; 869.0bp to feature; MODIFIER silent_mutation Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> A LOC_Os06g10850-LOC_Os06g10860 intergenic_region ; MODIFIER silent_mutation Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N
vg0605662134 G -> DEL N N silent_mutation Average:9.213; most accessible tissue: Callus, score: 19.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605662134 1.89E-06 NA mr1624_2 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