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Detailed information for vg0907121871:

Variant ID: vg0907121871 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7121871
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCAGTCCCAACCCTCCACCTAGGATGATGTCTATGGCATTAACTATATTGTCATGTAGGACTTTTAACTTATGTGGCACTATATTAATTAAGAGAGAGA[G/A]
TAAAGAGAAGAAGAAACTGAGTCTCATGCAAGACACAGCTTCAACACGAGAACCTATACACTAGACACTATCAAGTTTTGTATTGGGAGATAATAGTGTC

Reverse complement sequence

GACACTATTATCTCCCAATACAAAACTTGATAGTGTCTAGTGTATAGGTTCTCGTGTTGAAGCTGTGTCTTGCATGAGACTCAGTTTCTTCTTCTCTTTA[C/T]
TCTCTCTCTTAATTAATATAGTGCCACATAAGTTAAAAGTCCTACATGACAATATAGTTAATGCCATAGACATCATCCTAGGTGGAGGGTTGGGACTGCC

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 88.60% 1.00% 1.31% 9.12% NA
All Indica  2759 89.20% 0.00% 0.83% 9.97% NA
All Japonica  1512 84.70% 3.00% 2.45% 9.79% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 98.80% 0.00% 0.17% 1.01% NA
Indica II  465 97.20% 0.00% 0.00% 2.80% NA
Indica III  913 72.80% 0.00% 1.97% 25.19% NA
Indica Intermediate  786 96.20% 0.00% 0.51% 3.31% NA
Temperate Japonica  767 96.90% 0.00% 1.83% 1.30% NA
Tropical Japonica  504 75.40% 8.70% 2.78% 13.10% NA
Japonica Intermediate  241 65.60% 0.80% 3.73% 29.88% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 2.20% 2.22% 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
vg0907121871 G -> DEL N N silent_mutation Average:43.863; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N
vg0907121871 G -> A LOC_Os09g12430.1 upstream_gene_variant ; 4413.0bp to feature; MODIFIER silent_mutation Average:43.863; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N
vg0907121871 G -> A LOC_Os09g12440.1 upstream_gene_variant ; 1260.0bp to feature; MODIFIER silent_mutation Average:43.863; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N
vg0907121871 G -> A LOC_Os09g12450.1 downstream_gene_variant ; 1845.0bp to feature; MODIFIER silent_mutation Average:43.863; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N
vg0907121871 G -> A LOC_Os09g12440-LOC_Os09g12450 intergenic_region ; MODIFIER silent_mutation Average:43.863; most accessible tissue: Zhenshan97 root, score: 77.09 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907121871 NA 2.86E-07 mr1082 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
vg0907121871 5.99E-06 1.36E-08 mr1083 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
vg0907121871 1.92E-06 1.92E-06 mr1204 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
vg0907121871 NA 2.34E-08 mr1226 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
vg0907121871 1.45E-11 1.45E-11 mr1076_2 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
vg0907121871 3.04E-06 6.50E-10 mr1082_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
vg0907121871 6.67E-08 4.25E-12 mr1083_2 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
vg0907121871 6.94E-07 1.04E-06 mr1085_2 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
vg0907121871 6.42E-07 1.96E-08 mr1103_2 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
vg0907121871 7.23E-06 8.96E-08 mr1104_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
vg0907121871 4.59E-07 3.49E-08 mr1107_2 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
vg0907121871 3.72E-06 3.72E-06 mr1145_2 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
vg0907121871 1.22E-08 1.01E-11 mr1226_2 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
vg0907121871 1.13E-06 2.63E-09 mr1408_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