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Detailed information for vg0704618174:

Variant ID: vg0704618174 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4618174
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATATAATGTTTCTACGACCGAGATTGCGATAGGCCTATATTAATTATCCGAGTACTAATACGTCGAATGAGGTACAAAATAATACCTCACTTAACATAT[G/A]
AAATTGCGCAACAACCAACTTCAATACATTTTTATAACAATATTAACAAGTTTTACCAATAAATACTTCTTTATTTATTATTAACATAACATAGAAAAAT

Reverse complement sequence

ATTTTTCTATGTTATGTTAATAATAAATAAAGAAGTATTTATTGGTAAAACTTGTTAATATTGTTATAAAAATGTATTGAAGTTGGTTGTTGCGCAATTT[C/T]
ATATGTTAAGTGAGGTATTATTTTGTACCTCATTCGACGTATTAGTACTCGGATAATTAATATAGGCCTATCGCAATCTCGGTCGTAGAAACATTATATG

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 55.80% 32.70% 0.21% 11.26% NA
All Indica  2759 92.50% 2.30% 0.04% 5.15% NA
All Japonica  1512 0.50% 74.50% 0.40% 24.54% NA
Aus  269 16.40% 83.60% 0.00% 0.00% NA
Indica I  595 86.40% 0.70% 0.00% 12.94% NA
Indica II  465 97.20% 2.40% 0.00% 0.43% NA
Indica III  913 95.60% 1.60% 0.00% 2.74% NA
Indica Intermediate  786 90.70% 4.30% 0.13% 4.83% NA
Temperate Japonica  767 0.70% 55.50% 0.52% 43.29% NA
Tropical Japonica  504 0.40% 96.80% 0.40% 2.38% NA
Japonica Intermediate  241 0.40% 88.40% 0.00% 11.20% NA
VI/Aromatic  96 1.00% 83.30% 2.08% 13.54% NA
Intermediate  90 36.70% 55.60% 1.11% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0704618174 G -> DEL N N silent_mutation Average:35.908; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0704618174 G -> A LOC_Os07g08890.1 upstream_gene_variant ; 492.0bp to feature; MODIFIER silent_mutation Average:35.908; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0704618174 G -> A LOC_Os07g08880.1 downstream_gene_variant ; 3575.0bp to feature; MODIFIER silent_mutation Average:35.908; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0704618174 G -> A LOC_Os07g08880.2 downstream_gene_variant ; 3576.0bp to feature; MODIFIER silent_mutation Average:35.908; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0704618174 G -> A LOC_Os07g08880.3 downstream_gene_variant ; 3575.0bp to feature; MODIFIER silent_mutation Average:35.908; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0704618174 G -> A LOC_Os07g08880-LOC_Os07g08890 intergenic_region ; MODIFIER silent_mutation Average:35.908; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704618174 NA 1.22E-07 mr1045 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
vg0704618174 NA 2.39E-06 mr1058 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
vg0704618174 NA 1.33E-23 mr1083 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
vg0704618174 NA 3.42E-07 mr1083 Ind_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
vg0704618174 NA 2.89E-06 mr1103 Ind_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
vg0704618174 NA 6.05E-14 mr1138 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
vg0704618174 NA 2.78E-07 mr1138 Ind_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
vg0704618174 NA 1.91E-06 mr1176 Ind_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
vg0704618174 NA 2.21E-12 mr1195 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
vg0704618174 NA 9.52E-12 mr1233 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
vg0704618174 NA 3.11E-13 mr1270 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
vg0704618174 NA 8.80E-10 mr1299 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
vg0704618174 NA 2.16E-10 mr1316 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
vg0704618174 NA 6.98E-06 mr1398 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
vg0704618174 NA 1.58E-28 mr1436 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
vg0704618174 NA 7.15E-06 mr1436 Ind_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
vg0704618174 NA 7.74E-07 mr1560 Ind_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
vg0704618174 NA 9.50E-06 mr1568 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
vg0704618174 NA 3.31E-11 mr1578 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
vg0704618174 NA 1.35E-13 mr1655 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
vg0704618174 NA 3.09E-06 mr1661 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
vg0704618174 NA 3.70E-10 mr1663 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
vg0704618174 NA 9.01E-17 mr1700 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
vg0704618174 NA 1.14E-07 mr1716 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
vg0704618174 3.31E-07 NA mr1728 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
vg0704618174 9.77E-07 1.41E-08 mr1728 Ind_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
vg0704618174 NA 1.33E-06 mr1756 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
vg0704618174 NA 9.35E-12 mr1819 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
vg0704618174 NA 2.14E-06 mr1860 Ind_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