\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0108044840:

Variant ID: vg0108044840 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8044840
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGGAGCTTAGGGAAGGATTTGCACGCGACTAGGGAGAGAGAAAGCAGATGCACGTGCGGCCGAGGGAGATTCGCGCGCGACTGGAGAGAGAGGAAGCG[G/A]
ATGCGCTCAACCTGATAGGTTCGATGGTAGTGGTGGATAATTTGCATAAAATTTTTAAGGGTAGTGGGTCTTTAGCCGGACAATAATATGAAAAAAAAAC

Reverse complement sequence

GTTTTTTTTTCATATTATTGTCCGGCTAAAGACCCACTACCCTTAAAAATTTTATGCAAATTATCCACCACTACCATCGAACCTATCAGGTTGAGCGCAT[C/T]
CGCTTCCTCTCTCTCCAGTCGCGCGCGAATCTCCCTCGGCCGCACGTGCATCTGCTTTCTCTCTCCCTAGTCGCGTGCAAATCCTTCCCTAAGCTCCCAC

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 92.40% 7.60% 0.00% 0.00% NA
All Indica  2759 95.80% 4.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 11.90% 88.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 93.30% 6.70% 0.00% 0.00% NA
Indica Intermediate  786 94.50% 5.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0108044840 G -> A LOC_Os01g14360.1 upstream_gene_variant ; 3630.0bp to feature; MODIFIER silent_mutation Average:62.553; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0108044840 G -> A LOC_Os01g14370.1 downstream_gene_variant ; 2528.0bp to feature; MODIFIER silent_mutation Average:62.553; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0108044840 G -> A LOC_Os01g14370.2 downstream_gene_variant ; 2528.0bp to feature; MODIFIER silent_mutation Average:62.553; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0108044840 G -> A LOC_Os01g14360-LOC_Os01g14370 intergenic_region ; MODIFIER silent_mutation Average:62.553; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0108044840 NA 1.58E-17 mr1113 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
vg0108044840 NA 4.85E-18 mr1114 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
vg0108044840 NA 1.30E-21 mr1120 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
vg0108044840 NA 1.20E-21 mr1247 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
vg0108044840 NA 3.68E-06 mr1286 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
vg0108044840 NA 8.06E-06 mr1349 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
vg0108044840 NA 5.32E-19 mr1961 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
vg0108044840 9.05E-06 NA mr1068_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
vg0108044840 9.51E-09 NA mr1090_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
vg0108044840 NA 1.02E-21 mr1120_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
vg0108044840 NA 9.38E-23 mr1247_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
vg0108044840 NA 5.96E-10 mr1388_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
vg0108044840 NA 1.02E-18 mr1531_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
vg0108044840 NA 5.18E-14 mr1583_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
vg0108044840 NA 4.18E-06 mr1740_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
vg0108044840 NA 4.72E-15 mr1961_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