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Detailed information for vg0719447778:

Variant ID: vg0719447778 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19447778
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


TATTGAAGTGGTTTACTATTAATCTAGTCTATTGTTGAGGTGTACATGTTTTATAGATAGCACCTTACTTTACCATTGCGGGTGCTCTAATTCTGCATTT[C/G]
TGCTGCTCCGGCGGCCAGAGCGTGGAGAGATAATAACGTCTTCAGTCCGTTGGTGCCAATGCACACGCCTAGGACTTGATTAGTGTTTGCAGATCGTATA

Reverse complement sequence

TATACGATCTGCAAACACTAATCAAGTCCTAGGCGTGTGCATTGGCACCAACGGACTGAAGACGTTATTATCTCTCCACGCTCTGGCCGCCGGAGCAGCA[G/C]
AAATGCAGAATTAGAGCACCCGCAATGGTAAAGTAAGGTGCTATCTATAAAACATGTACACCTCAACAATAGACTAGATTAATAGTAAACCACTTCAATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.80% 38.20% 13.84% 1.16% NA
All Indica  2759 56.00% 18.90% 23.20% 1.92% NA
All Japonica  1512 35.10% 64.90% 0.07% 0.00% NA
Aus  269 23.80% 76.20% 0.00% 0.00% NA
Indica I  595 38.70% 25.00% 33.61% 2.69% NA
Indica II  465 50.50% 19.40% 27.96% 2.15% NA
Indica III  913 70.90% 13.60% 13.69% 1.86% NA
Indica Intermediate  786 55.00% 20.20% 23.54% 1.27% NA
Temperate Japonica  767 4.20% 95.80% 0.00% 0.00% NA
Tropical Japonica  504 79.00% 20.80% 0.20% 0.00% NA
Japonica Intermediate  241 41.50% 58.50% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 53.30% 30.00% 14.44% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0719447778 C -> DEL N N silent_mutation Average:37.832; most accessible tissue: Callus, score: 86.738 N N N N
vg0719447778 C -> G LOC_Os07g32610.2 upstream_gene_variant ; 1834.0bp to feature; MODIFIER silent_mutation Average:37.832; most accessible tissue: Callus, score: 86.738 N N N N
vg0719447778 C -> G LOC_Os07g32610.1 upstream_gene_variant ; 2149.0bp to feature; MODIFIER silent_mutation Average:37.832; most accessible tissue: Callus, score: 86.738 N N N N
vg0719447778 C -> G LOC_Os07g32610-LOC_Os07g32620 intergenic_region ; MODIFIER silent_mutation Average:37.832; most accessible tissue: Callus, score: 86.738 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719447778 NA 1.86E-06 mr1031 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
vg0719447778 NA 1.39E-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
vg0719447778 NA 3.44E-06 mr1056 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
vg0719447778 NA 7.84E-07 mr1213 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
vg0719447778 NA 3.66E-08 mr1295 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
vg0719447778 NA 9.16E-20 mr1422 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
vg0719447778 NA 9.34E-07 mr1780 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
vg0719447778 NA 7.61E-06 mr1088_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
vg0719447778 NA 2.79E-14 mr1147_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
vg0719447778 3.39E-06 NA mr1224_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
vg0719447778 NA 5.30E-08 mr1224_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
vg0719447778 NA 3.36E-09 mr1246_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
vg0719447778 5.88E-06 2.01E-13 mr1248_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
vg0719447778 2.75E-06 NA mr1257_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
vg0719447778 NA 7.14E-09 mr1364_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
vg0719447778 NA 1.73E-07 mr1404_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
vg0719447778 NA 2.76E-07 mr1498_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
vg0719447778 9.66E-06 3.28E-06 mr1519_2 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
vg0719447778 NA 4.69E-06 mr1620_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
vg0719447778 NA 2.06E-07 mr1629_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