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Detailed information for vg1000551614:

Variant ID: vg1000551614 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 551614
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, G: 0.28, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTAGGTGCCGATGACATATCATTTATCTATAGGCCGATGTCATATGTACATTGATCGGCAAGTGTTAATAAGCAAATCAAAACTAAATCTACCCGATC[A/G]
GCTGTAGATATTAATGATATATAATCCTTATATCGATATATACTTAAATCAAGTGATTGGGATAGATCGGTCATCTTGCCGAGACAGTATAAATCACTTA

Reverse complement sequence

TAAGTGATTTATACTGTCTCGGCAAGATGACCGATCTATCCCAATCACTTGATTTAAGTATATATCGATATAAGGATTATATATCATTAATATCTACAGC[T/C]
GATCGGGTAGATTTAGTTTTGATTTGCTTATTAACACTTGCCGATCAATGTACATATGACATCGGCCTATAGATAAATGATATGTCATCGGCACCTAGCC

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 17.40% 1.70% 16.63% 64.30% NA
All Indica  2759 1.20% 0.10% 27.76% 70.90% NA
All Japonica  1512 49.70% 4.80% 0.60% 44.97% NA
Aus  269 3.70% 0.40% 0.37% 95.54% NA
Indica I  595 1.50% 0.00% 22.86% 75.63% NA
Indica II  465 1.70% 0.00% 18.28% 80.00% NA
Indica III  913 0.30% 0.00% 41.18% 58.49% NA
Indica Intermediate  786 1.80% 0.40% 21.50% 76.34% NA
Temperate Japonica  767 78.60% 8.60% 0.13% 12.65% NA
Tropical Japonica  504 7.30% 0.00% 1.59% 91.07% NA
Japonica Intermediate  241 46.10% 2.50% 0.00% 51.45% NA
VI/Aromatic  96 9.40% 0.00% 0.00% 90.62% NA
Intermediate  90 20.00% 3.30% 11.11% 65.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000551614 A -> G LOC_Os10g01844.1 upstream_gene_variant ; 2821.0bp to feature; MODIFIER silent_mutation Average:13.483; most accessible tissue: Callus, score: 25.831 N N N N
vg1000551614 A -> G LOC_Os10g01850.1 intron_variant ; MODIFIER silent_mutation Average:13.483; most accessible tissue: Callus, score: 25.831 N N N N
vg1000551614 A -> DEL N N silent_mutation Average:13.483; most accessible tissue: Callus, score: 25.831 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000551614 1.12E-06 NA mr1757 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
vg1000551614 NA 8.59E-10 mr1757 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
vg1000551614 1.89E-10 NA mr1310_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
vg1000551614 1.15E-09 NA mr1310_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
vg1000551614 NA 2.12E-06 mr1354_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
vg1000551614 NA 2.19E-08 mr1549_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
vg1000551614 NA 3.79E-07 mr1757_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
vg1000551614 4.74E-07 NA mr1959_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