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Detailed information for vg0720910687:

Variant ID: vg0720910687 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20910687
Reference Allele: AAlternative Allele: G,C
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTGAAACAAGATTAAAACATATTGCATTGTAATATGGAGAACCAGTTGCTCTTGATACAAATCGAACAGGAGAACATTAACAATATTAAAAAACTATA[A/G,C]
AAACAAAAATTTGATAGATGAAGGTCAGAAATGGTATGAATGACTACATACCTACCAGTCTTATAAATCCAACCTGAATACAAAATGGCTGTATTTTACA

Reverse complement sequence

TGTAAAATACAGCCATTTTGTATTCAGGTTGGATTTATAAGACTGGTAGGTATGTAGTCATTCATACCATTTCTGACCTTCATCTATCAAATTTTTGTTT[T/C,G]
TATAGTTTTTTAATATTGTTAATGTTCTCCTGTTCGATTTGTATCAAGAGCAACTGGTTCTCCATATTACAATGCAATATGTTTTAATCTTGTTTCACAT

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 44.80% 14.90% 7.64% 31.78% C: 0.87%
All Indica  2759 26.70% 8.60% 10.44% 52.85% C: 1.45%
All Japonica  1512 84.40% 15.10% 0.26% 0.20% NA
Aus  269 2.60% 76.20% 13.75% 7.43% NA
Indica I  595 20.50% 1.00% 4.03% 74.45% NA
Indica II  465 19.80% 4.10% 10.11% 65.38% C: 0.65%
Indica III  913 28.30% 16.80% 18.07% 33.52% C: 3.40%
Indica Intermediate  786 33.70% 7.40% 6.62% 51.53% C: 0.76%
Temperate Japonica  767 82.70% 16.70% 0.26% 0.39% NA
Tropical Japonica  504 83.10% 16.70% 0.20% 0.00% NA
Japonica Intermediate  241 92.50% 7.10% 0.41% 0.00% NA
VI/Aromatic  96 44.80% 24.00% 30.21% 0.00% C: 1.04%
Intermediate  90 61.10% 12.20% 3.33% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0720910687 A -> DEL N N silent_mutation Average:11.288; most accessible tissue: Callus, score: 67.906 N N N N
vg0720910687 A -> G LOC_Os07g34890.1 upstream_gene_variant ; 1521.0bp to feature; MODIFIER silent_mutation Average:11.288; most accessible tissue: Callus, score: 67.906 N N N N
vg0720910687 A -> G LOC_Os07g34880.1 downstream_gene_variant ; 4855.0bp to feature; MODIFIER silent_mutation Average:11.288; most accessible tissue: Callus, score: 67.906 N N N N
vg0720910687 A -> G LOC_Os07g34880-LOC_Os07g34890 intergenic_region ; MODIFIER silent_mutation Average:11.288; most accessible tissue: Callus, score: 67.906 N N N N
vg0720910687 A -> C LOC_Os07g34890.1 upstream_gene_variant ; 1521.0bp to feature; MODIFIER silent_mutation Average:11.288; most accessible tissue: Callus, score: 67.906 N N N N
vg0720910687 A -> C LOC_Os07g34880.1 downstream_gene_variant ; 4855.0bp to feature; MODIFIER silent_mutation Average:11.288; most accessible tissue: Callus, score: 67.906 N N N N
vg0720910687 A -> C LOC_Os07g34880-LOC_Os07g34890 intergenic_region ; MODIFIER silent_mutation Average:11.288; most accessible tissue: Callus, score: 67.906 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720910687 NA 3.30E-07 mr1057_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
vg0720910687 1.62E-06 NA mr1807_2 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