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Detailed information for vg0311501408:

Variant ID: vg0311501408 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 11501408
Reference Allele: GAlternative Allele: A,GA
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATACGAGTATCCGTGTTAAATTTAGAATTTGAACCCATGTGAGTCGATTCAAGAGCTATACACTCACTTGGCATCTAGGCGTATTATCCTGATTTTACAC[G/A,GA]
ATAAAAAAAACAATTGCATGTGCTCCATCTATTCCAACCCAAGTTTTATCCTAAATCAAACAAATATACATTTTTACCATTAATTTTTAAATATAGTTTA

Reverse complement sequence

TAAACTATATTTAAAAATTAATGGTAAAAATGTATATTTGTTTGATTTAGGATAAAACTTGGGTTGGAATAGATGGAGCACATGCAATTGTTTTTTTTAT[C/T,TC]
GTGTAAAATCAGGATAATACGCCTAGATGCCAAGTGAGTGTATAGCTCTTGAATCGACTCACATGGGTTCAAATTCTAAATTTAACACGGATACTCGTAT

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 87.50% 7.10% 5.01% 0.34% GA: 0.02%
All Indica  2759 99.70% 0.00% 0.14% 0.07% GA: 0.04%
All Japonica  1512 62.20% 21.80% 15.21% 0.86% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.00% 0.25% 0.13% GA: 0.13%
Temperate Japonica  767 39.40% 37.30% 23.34% 0.00% NA
Tropical Japonica  504 90.90% 1.00% 6.15% 1.98% NA
Japonica Intermediate  241 74.70% 15.80% 8.30% 1.24% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 8.90% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0311501408 G -> GA LOC_Os03g20330.1 downstream_gene_variant ; 2732.0bp to feature; MODIFIER silent_mutation Average:52.4; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg0311501408 G -> GA LOC_Os03g20330-LOC_Os03g20340 intergenic_region ; MODIFIER silent_mutation Average:52.4; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg0311501408 G -> A LOC_Os03g20330.1 downstream_gene_variant ; 2731.0bp to feature; MODIFIER silent_mutation Average:52.4; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg0311501408 G -> A LOC_Os03g20330-LOC_Os03g20340 intergenic_region ; MODIFIER silent_mutation Average:52.4; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N
vg0311501408 G -> DEL N N silent_mutation Average:52.4; most accessible tissue: Zhenshan97 root, score: 79.452 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0311501408 NA 2.96E-06 mr1069 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
vg0311501408 NA 9.50E-07 mr1748 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
vg0311501408 NA 8.63E-06 mr1837 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
vg0311501408 NA 1.77E-07 mr1880 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
vg0311501408 3.75E-07 1.90E-08 mr1955 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