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Detailed information for vg0515214255:

Variant ID: vg0515214255 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 15214255
Reference Allele: CATGTCAGTTACATAGTAGTTACAATTTAATTATAlternative Allele: C
Primary Allele: CATGTCAGTTACATAGTAGT TACAATTTAATTATSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGCAGGATCGAACCCAACACCTACAACTTGGAGGTTTGTTCAACTAACCAGTTGCTCCATCATGCTTTTTTTAGCAACACTCGAGTTATATATCAGTTA[CATGTCAGTTACATAGTAGTTACAATTTAATTAT/C]
ATAGTAGTTACATTTGAAAGTTTTTCATCCAAAAACTGTCGACAGTTGTATAGCTACTCCCTACATATATATATATACACACGCAAAGGTATTAGGAAAA

Reverse complement sequence

TTTTCCTAATACCTTTGCGTGTGTATATATATATATGTAGGGAGTAGCTATACAACTGTCGACAGTTTTTGGATGAAAAACTTTCAAATGTAACTACTAT[ATAATTAAATTGTAACTACTATGTAACTGACATG/G]
TAACTGATATATAACTCGAGTGTTGCTAAAAAAAGCATGATGGAGCAACTGGTTAGTTGAACAAACCTCCAAGTTGTAGGTGTTGGGTTCGATCCTGCTG

Allele Frequencies:

Populations Population SizeFrequency of CATGTCAGTTACATAGTAGT TACAATTTAATTAT(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.60% 0.10% 0.34% 40.92% NA
All Indica  2759 44.30% 0.00% 0.47% 55.20% NA
All Japonica  1512 77.50% 0.30% 0.13% 22.02% NA
Aus  269 80.30% 0.00% 0.37% 19.33% NA
Indica I  595 26.10% 0.00% 0.50% 73.45% NA
Indica II  465 63.00% 0.00% 0.00% 36.99% NA
Indica III  913 54.40% 0.00% 0.44% 45.13% NA
Indica Intermediate  786 35.40% 0.00% 0.76% 63.87% NA
Temperate Japonica  767 93.50% 0.70% 0.13% 5.74% NA
Tropical Japonica  504 52.00% 0.00% 0.20% 47.82% NA
Japonica Intermediate  241 80.10% 0.00% 0.00% 19.92% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 71.10% 0.00% 0.00% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0515214255 CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> DEL N N silent_mutation Average:20.529; most accessible tissue: Callus, score: 88.602 N N N N
vg0515214255 CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> C LOC_Os05g26140.1 upstream_gene_variant ; 1826.0bp to feature; MODIFIER silent_mutation Average:20.529; most accessible tissue: Callus, score: 88.602 N N N N
vg0515214255 CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> C LOC_Os05g26150.1 upstream_gene_variant ; 4104.0bp to feature; MODIFIER silent_mutation Average:20.529; most accessible tissue: Callus, score: 88.602 N N N N
vg0515214255 CATGTCAGTTACATAGTAGTTACAATTTAATTAT -> C LOC_Os05g26140-LOC_Os05g26150 intergenic_region ; MODIFIER silent_mutation Average:20.529; most accessible tissue: Callus, score: 88.602 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515214255 NA 8.96E-06 mr1113 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
vg0515214255 2.19E-06 5.68E-08 mr1114 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
vg0515214255 NA 2.31E-06 mr1116 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
vg0515214255 8.32E-06 1.07E-07 mr1117 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
vg0515214255 NA 3.82E-08 mr1118 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
vg0515214255 NA 2.76E-06 mr1119 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
vg0515214255 5.59E-06 6.44E-09 mr1123 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
vg0515214255 NA 5.84E-06 mr1240 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
vg0515214255 8.19E-07 7.75E-10 mr1242 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
vg0515214255 3.66E-06 3.16E-08 mr1496 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
vg0515214255 NA 5.89E-09 mr1693 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
vg0515214255 NA 1.21E-06 mr1113_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
vg0515214255 4.15E-06 2.81E-07 mr1114_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
vg0515214255 9.72E-06 1.14E-07 mr1117_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
vg0515214255 1.48E-06 4.38E-09 mr1118_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
vg0515214255 7.88E-06 1.16E-07 mr1119_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
vg0515214255 NA 1.58E-06 mr1120_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
vg0515214255 NA 1.32E-07 mr1123_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
vg0515214255 7.29E-07 5.59E-09 mr1240_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
vg0515214255 8.05E-06 3.02E-08 mr1242_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
vg0515214255 NA 1.82E-06 mr1247_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
vg0515214255 3.95E-08 2.98E-11 mr1496_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