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Detailed information for vg1001389874:

Variant ID: vg1001389874 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1389874
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACTCTGCTGCGTGCTCTGATCTGCTTATAGTTCCACAATCCCATATCCAACATCTACACAATTTACACGCCGTCACCGGGGCGCACACATGTACACGCC[A/G]
CCGCCAAGCGCTGCGCCAAGATGCAGGCCCTGAGCTGGTGATGGTGAATATGATAGCCACACAAATATTTGGGAGGAATCGGGAGAAGGCAAAGTAATCA

Reverse complement sequence

TGATTACTTTGCCTTCTCCCGATTCCTCCCAAATATTTGTGTGGCTATCATATTCACCATCACCAGCTCAGGGCCTGCATCTTGGCGCAGCGCTTGGCGG[T/C]
GGCGTGTACATGTGTGCGCCCCGGTGACGGCGTGTAAATTGTGTAGATGTTGGATATGGGATTGTGGAACTATAAGCAGATCAGAGCACGCAGCAGAGTT

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 84.10% 13.30% 2.54% 0.00% NA
All Indica  2759 95.40% 0.90% 3.70% 0.00% NA
All Japonica  1512 61.20% 38.60% 0.20% 0.00% NA
Aus  269 95.50% 1.90% 2.60% 0.00% NA
Indica I  595 96.60% 2.00% 1.34% 0.00% NA
Indica II  465 98.90% 0.40% 0.65% 0.00% NA
Indica III  913 92.80% 0.20% 7.01% 0.00% NA
Indica Intermediate  786 95.40% 1.10% 3.44% 0.00% NA
Temperate Japonica  767 28.80% 71.10% 0.13% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 86.70% 12.40% 0.83% 0.00% NA
VI/Aromatic  96 89.60% 3.10% 7.29% 0.00% NA
Intermediate  90 84.40% 14.40% 1.11% 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
vg1001389874 A -> G LOC_Os10g03270.1 upstream_gene_variant ; 4299.0bp to feature; MODIFIER silent_mutation Average:30.561; most accessible tissue: Zhenshan97 root, score: 50.453 N N N N
vg1001389874 A -> G LOC_Os10g03290.1 upstream_gene_variant ; 939.0bp to feature; MODIFIER silent_mutation Average:30.561; most accessible tissue: Zhenshan97 root, score: 50.453 N N N N
vg1001389874 A -> G LOC_Os10g03280.1 downstream_gene_variant ; 688.0bp to feature; MODIFIER silent_mutation Average:30.561; most accessible tissue: Zhenshan97 root, score: 50.453 N N N N
vg1001389874 A -> G LOC_Os10g03280-LOC_Os10g03290 intergenic_region ; MODIFIER silent_mutation Average:30.561; most accessible tissue: Zhenshan97 root, score: 50.453 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001389874 NA 5.41E-06 mr1011 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
vg1001389874 NA 8.39E-07 mr1026 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
vg1001389874 NA 8.80E-07 mr1063 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
vg1001389874 NA 4.51E-07 mr1206 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
vg1001389874 1.51E-06 1.39E-24 mr1300 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
vg1001389874 NA 1.14E-35 mr1310 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
vg1001389874 NA 7.74E-07 mr1310 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
vg1001389874 NA 4.25E-06 mr1330 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
vg1001389874 1.23E-07 4.01E-43 mr1486 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
vg1001389874 4.65E-06 1.71E-15 mr1486 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
vg1001389874 NA 5.31E-23 mr1548 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
vg1001389874 NA 6.69E-10 mr1548 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
vg1001389874 NA 2.20E-09 mr1570 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
vg1001389874 NA 1.27E-08 mr1627 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
vg1001389874 NA 8.61E-07 mr1668 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
vg1001389874 NA 3.96E-22 mr1920 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
vg1001389874 1.89E-06 9.68E-42 mr1926 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
vg1001389874 NA 9.27E-13 mr1959 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
vg1001389874 NA 1.61E-06 mr1977 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
vg1001389874 NA 9.81E-06 mr1977 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
vg1001389874 NA 4.78E-06 mr1063_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
vg1001389874 NA 1.96E-06 mr1161_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
vg1001389874 2.71E-07 4.54E-39 mr1310_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
vg1001389874 NA 7.40E-10 mr1310_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
vg1001389874 1.02E-13 7.26E-55 mr1486_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
vg1001389874 8.93E-11 4.27E-20 mr1486_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
vg1001389874 NA 7.69E-06 mr1588_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
vg1001389874 NA 1.89E-18 mr1959_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
vg1001389874 NA 1.74E-06 mr1959_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