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Detailed information for vg0323687205:

Variant ID: vg0323687205 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23687205
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATATTCTTTTAGAGAGAGTGTGACTGTGTGAGAGATAGAAACTAGAGAGAGAGAGTAGTTAATTTCTATCAAATCCTTTCACGGGCCGTTTGGTTAGG[A/G]
GGAGTTTTTAGGAGGGATTAGGAGTTTAGTGGGATGAGGATATTAACTACTCCCTCCGTATTTTAATGTATGACGTTGTTGACTTTTCGACAAACGTTTG

Reverse complement sequence

CAAACGTTTGTCGAAAAGTCAACAACGTCATACATTAAAATACGGAGGGAGTAGTTAATATCCTCATCCCACTAAACTCCTAATCCCTCCTAAAAACTCC[T/C]
CCTAACCAAACGGCCCGTGAAAGGATTTGATAGAAATTAACTACTCTCTCTCTCTAGTTTCTATCTCTCACACAGTCACACTCTCTCTAAAAGAATATAT

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 86.90% 13.00% 0.08% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 65.90% 33.80% 0.26% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 48.80% 51.10% 0.13% 0.00% NA
Tropical Japonica  504 87.90% 12.10% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 24.10% 1.24% 0.00% NA
VI/Aromatic  96 38.50% 61.50% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0323687205 A -> G LOC_Os03g42550.1 upstream_gene_variant ; 2289.0bp to feature; MODIFIER silent_mutation Average:45.113; most accessible tissue: Zhenshan97 flower, score: 60.301 N N N N
vg0323687205 A -> G LOC_Os03g42540-LOC_Os03g42550 intergenic_region ; MODIFIER silent_mutation Average:45.113; most accessible tissue: Zhenshan97 flower, score: 60.301 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323687205 5.11E-06 NA mr1305_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
vg0323687205 4.72E-06 NA mr1305_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
vg0323687205 2.75E-06 NA mr1379_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
vg0323687205 NA 1.40E-07 mr1379_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
vg0323687205 5.42E-06 2.02E-07 mr1409_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
vg0323687205 3.15E-06 NA mr1559_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
vg0323687205 NA 1.19E-07 mr1559_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
vg0323687205 4.83E-07 NA mr1585_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
vg0323687205 2.26E-06 2.26E-06 mr1649_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
vg0323687205 NA 1.70E-06 mr1768_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