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Detailed information for vg1001004126:

Variant ID: vg1001004126 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1004126
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAATCGTTGATTTTACTCCAGCCAGATTTGTATATTAAGTTACAATCAATGTACAATTATGATAAAATCTCCCAGATAATTCCGTTCACAATCTATCTA[A/G]
TTAATGCGTGGGCGTTTCGATATGATCCAAAGATATCTCACATCTATTTCGTCTATAAATGCAAAATTAATTGTAATATACTATATATATTCGTCGGCCA

Reverse complement sequence

TGGCCGACGAATATATATAGTATATTACAATTAATTTTGCATTTATAGACGAAATAGATGTGAGATATCTTTGGATCATATCGAAACGCCCACGCATTAA[T/C]
TAGATAGATTGTGAACGGAATTATCTGGGAGATTTTATCATAATTGTACATTGATTGTAACTTAATATACAAATCTGGCTGGAGTAAAATCAACGATTGC

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 99.00% 0.60% 0.32% 0.00% NA
All Indica  2759 99.90% 0.00% 0.11% 0.00% NA
All Japonica  1512 97.40% 2.00% 0.66% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 95.70% 3.40% 0.91% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg1001004126 A -> G LOC_Os10g02620.1 upstream_gene_variant ; 1219.0bp to feature; MODIFIER silent_mutation Average:52.253; most accessible tissue: Zhenshan97 flower, score: 74.205 N N N N
vg1001004126 A -> G LOC_Os10g02625.1 upstream_gene_variant ; 150.0bp to feature; MODIFIER silent_mutation Average:52.253; most accessible tissue: Zhenshan97 flower, score: 74.205 N N N N
vg1001004126 A -> G LOC_Os10g02610.1 downstream_gene_variant ; 4675.0bp to feature; MODIFIER silent_mutation Average:52.253; most accessible tissue: Zhenshan97 flower, score: 74.205 N N N N
vg1001004126 A -> G LOC_Os10g02630.1 downstream_gene_variant ; 3460.0bp to feature; MODIFIER silent_mutation Average:52.253; most accessible tissue: Zhenshan97 flower, score: 74.205 N N N N
vg1001004126 A -> G LOC_Os10g02620-LOC_Os10g02625 intergenic_region ; MODIFIER silent_mutation Average:52.253; most accessible tissue: Zhenshan97 flower, score: 74.205 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001004126 2.64E-06 2.64E-06 mr1412 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
vg1001004126 NA 1.00E-08 mr1549 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
vg1001004126 NA 2.09E-06 mr1550 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
vg1001004126 NA 4.99E-08 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
vg1001004126 NA 7.43E-06 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