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Detailed information for vg0621396414:

Variant ID: vg0621396414 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21396414
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTGGAGGCAGAGGAGAAAGACATTTTCATAATAGTATATAGAGTATTTACTGTAAAACTATTCTAATTCTCAAGGGCATATCTTCTTGTTATTTGCAT[A/G]
TTAATTAAATAACTATAAAAAATTTAAAAAGATGCATTAATATACTACTTCAGTCCCATAATAGATGTTGCTTTGACTTTCTGCTTACAATATTTGACCA

Reverse complement sequence

TGGTCAAATATTGTAAGCAGAAAGTCAAAGCAACATCTATTATGGGACTGAAGTAGTATATTAATGCATCTTTTTAAATTTTTTATAGTTATTTAATTAA[T/C]
ATGCAAATAACAAGAAGATATGCCCTTGAGAATTAGAATAGTTTTACAGTAAATACTCTATATACTATTATGAAAATGTCTTTCTCCTCTGCCTCCACAT

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 68.90% 31.00% 0.06% 0.00% NA
All Indica  2759 98.60% 1.40% 0.04% 0.00% NA
All Japonica  1512 9.50% 90.30% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.50% 0.13% 0.00% NA
Temperate Japonica  767 5.90% 93.90% 0.26% 0.00% NA
Tropical Japonica  504 15.90% 84.10% 0.00% 0.00% NA
Japonica Intermediate  241 7.90% 92.10% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg0621396414 A -> G LOC_Os06g36440.1 upstream_gene_variant ; 1752.0bp to feature; MODIFIER silent_mutation Average:35.744; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0621396414 A -> G LOC_Os06g36450.1 upstream_gene_variant ; 410.0bp to feature; MODIFIER silent_mutation Average:35.744; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0621396414 A -> G LOC_Os06g36460.1 upstream_gene_variant ; 4422.0bp to feature; MODIFIER silent_mutation Average:35.744; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0621396414 A -> G LOC_Os06g36430.1 downstream_gene_variant ; 3904.0bp to feature; MODIFIER silent_mutation Average:35.744; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0621396414 A -> G LOC_Os06g36440-LOC_Os06g36450 intergenic_region ; MODIFIER silent_mutation Average:35.744; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621396414 NA 4.95E-16 mr1010 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
vg0621396414 9.55E-08 1.85E-08 mr1010 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
vg0621396414 NA 8.17E-22 mr1163 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
vg0621396414 NA 2.64E-06 mr1510 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
vg0621396414 NA 7.08E-10 mr1905 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
vg0621396414 NA 2.14E-22 mr1010_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
vg0621396414 NA 4.19E-25 mr1024_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
vg0621396414 NA 1.07E-21 mr1276_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
vg0621396414 NA 3.90E-15 mr1324_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
vg0621396414 NA 8.73E-07 mr1369_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
vg0621396414 NA 2.20E-07 mr1453_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
vg0621396414 NA 1.39E-17 mr1682_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
vg0621396414 2.21E-06 NA mr1842_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
vg0621396414 NA 4.13E-21 mr1968_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