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Detailed information for vg0419885029:

Variant ID: vg0419885029 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 19885029
Reference Allele: AAlternative Allele: T,ACT,ACACTCT
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCATCTAATTCCATTTTGTTATCATTTTCTCAAGACTTCTCCTGTGAATATGTGATGATGTAATCAATATGTACTCCCTCAGGCAATTGACACACACAC[A/T,ACT,ACACTCT]
CTCTCTCTCCTATGATATACATACTTGATTATTTTTCTAGACATATATTTATATAGATTACTAAAATATAACTAAAAAAATAATTCCTTAATGAAAAATC

Reverse complement sequence

GATTTTTCATTAAGGAATTATTTTTTTAGTTATATTTTAGTAATCTATATAAATATATGTCTAGAAAAATAATCAAGTATGTATATCATAGGAGAGAGAG[T/A,AGT,AGAGTGT]
GTGTGTGTGTCAATTGCCTGAGGGAGTACATATTGATTACATCATCACATATTCACAGGAGAAGTCTTGAGAAAATGATAACAAAATGGAATTAGATGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.60% 18.40% 1.23% 0.00% ACT: 5.69%; ACACTCT: 0.11%
All Indica  2759 66.70% 21.80% 1.81% 0.00% ACT: 9.50%; ACACTCT: 0.14%
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 10.00% 88.50% 1.49% 0.00% NA
Indica I  595 82.00% 12.30% 2.69% 0.00% ACT: 3.03%
Indica II  465 48.80% 7.30% 2.58% 0.00% ACT: 41.29%
Indica III  913 62.00% 36.90% 0.55% 0.00% ACACTCT: 0.44%; ACT: 0.11%
Indica Intermediate  786 71.20% 20.10% 2.16% 0.00% ACT: 6.49%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 82.20% 5.60% 3.33% 0.00% ACT: 7.78%; ACACTCT: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0419885029 A -> ACACTCT LOC_Os04g32910.1 upstream_gene_variant ; 459.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACACTCT LOC_Os04g32920.1 upstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACACTCT LOC_Os04g32920.3 upstream_gene_variant ; 1644.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACACTCT LOC_Os04g32920.2 upstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACACTCT LOC_Os04g32920.5 upstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACACTCT LOC_Os04g32920.4 upstream_gene_variant ; 2910.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACACTCT LOC_Os04g32910-LOC_Os04g32920 intergenic_region ; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACT LOC_Os04g32910.1 upstream_gene_variant ; 459.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACT LOC_Os04g32920.1 upstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACT LOC_Os04g32920.3 upstream_gene_variant ; 1644.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACT LOC_Os04g32920.2 upstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACT LOC_Os04g32920.5 upstream_gene_variant ; 1646.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACT LOC_Os04g32920.4 upstream_gene_variant ; 2910.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> ACT LOC_Os04g32910-LOC_Os04g32920 intergenic_region ; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> T LOC_Os04g32910.1 upstream_gene_variant ; 458.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> T LOC_Os04g32920.1 upstream_gene_variant ; 1647.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> T LOC_Os04g32920.3 upstream_gene_variant ; 1645.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> T LOC_Os04g32920.2 upstream_gene_variant ; 1647.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> T LOC_Os04g32920.5 upstream_gene_variant ; 1647.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> T LOC_Os04g32920.4 upstream_gene_variant ; 2911.0bp to feature; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N
vg0419885029 A -> T LOC_Os04g32910-LOC_Os04g32920 intergenic_region ; MODIFIER silent_mutation Average:49.882; most accessible tissue: Zhenshan97 root, score: 86.991 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419885029 NA 5.47E-07 mr1028 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
vg0419885029 NA 6.92E-07 mr1369 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
vg0419885029 NA 7.13E-08 mr1453 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
vg0419885029 NA 8.26E-07 mr1556 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
vg0419885029 NA 2.27E-08 mr1764 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
vg0419885029 NA 2.19E-06 mr1931 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
vg0419885029 NA 3.43E-17 mr1240_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
vg0419885029 3.55E-06 9.66E-07 mr1950_2 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