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Detailed information for vg0713004172:

Variant ID: vg0713004172 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 13004172
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATCAATCGACGAGCCCCTAGTGCTCTTGCCTTTCTCATGGCTAATAAAACCCCTTCATATTCTGCCGTGTTGTTTGTTGATGGGAAAACTAGCTTTGCA[A/G]
AATATTTTAGTGTTTGCTTCATCGGCGTTTTTACAACCACTGCTGCCCCTACGCCAGTGGCATTGCATGCTCCATCAGAGTATATTATCCATAGTTTTTC

Reverse complement sequence

GAAAAACTATGGATAATATACTCTGATGGAGCATGCAATGCCACTGGCGTAGGGGCAGCAGTGGTTGTAAAAACGCCGATGAAGCAAACACTAAAATATT[T/C]
TGCAAAGCTAGTTTTCCCATCAACAAACAACACGGCAGAATATGAAGGGGTTTTATTAGCCATGAGAAAGGCAAGAGCACTAGGGGCTCGTCGATTGATA

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 55.40% 1.10% 0.57% 42.89% NA
All Indica  2759 39.00% 0.40% 0.80% 59.84% NA
All Japonica  1512 92.00% 0.10% 0.13% 7.80% NA
Aus  269 25.70% 15.20% 0.74% 58.36% NA
Indica I  595 74.10% 0.00% 0.34% 25.55% NA
Indica II  465 43.40% 0.40% 1.08% 55.05% NA
Indica III  913 8.10% 0.50% 0.88% 90.47% NA
Indica Intermediate  786 45.50% 0.50% 0.89% 53.05% NA
Temperate Japonica  767 93.50% 0.00% 0.13% 6.39% NA
Tropical Japonica  504 90.90% 0.00% 0.20% 8.93% NA
Japonica Intermediate  241 89.60% 0.40% 0.00% 9.96% NA
VI/Aromatic  96 29.20% 0.00% 0.00% 70.83% NA
Intermediate  90 61.10% 1.10% 1.11% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0713004172 A -> DEL N N silent_mutation Average:8.481; most accessible tissue: Callus, score: 38.589 N N N N
vg0713004172 A -> G LOC_Os07g23040.1 upstream_gene_variant ; 167.0bp to feature; MODIFIER silent_mutation Average:8.481; most accessible tissue: Callus, score: 38.589 N N N N
vg0713004172 A -> G LOC_Os07g23050.1 downstream_gene_variant ; 540.0bp to feature; MODIFIER silent_mutation Average:8.481; most accessible tissue: Callus, score: 38.589 N N N N
vg0713004172 A -> G LOC_Os07g23040-LOC_Os07g23050 intergenic_region ; MODIFIER silent_mutation Average:8.481; most accessible tissue: Callus, score: 38.589 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0713004172 NA 2.13E-08 mr1078 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
vg0713004172 NA 6.88E-07 mr1289 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
vg0713004172 1.65E-06 3.05E-07 mr1289 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
vg0713004172 NA 8.74E-06 mr1474 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
vg0713004172 NA 8.74E-06 mr1475 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
vg0713004172 NA 6.79E-06 mr1695 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
vg0713004172 NA 1.19E-06 mr1746 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
vg0713004172 NA 8.10E-07 mr1788 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
vg0713004172 NA 4.60E-06 mr1798 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
vg0713004172 6.97E-06 NA mr1881 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
vg0713004172 NA 4.93E-06 mr1981 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
vg0713004172 NA 9.57E-07 mr1321_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