Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0117431722:

Variant ID: vg0117431722 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 17431722
Reference Allele: AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGCAlternative Allele: GACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC,A
Primary Allele: AACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGCSecondary Allele: GACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTCATATCAACAAGTTGCAACTTCTTTTCCGGAATCCAATCTCCAAAGAACTCCAGGGTTAAGCGTGCTTGGCCTGGAGCAATTTGGGATGGGTGACC[AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC/GACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC,A]
AGAAAAGATATGTGTTGGTCTGTGAGGGCAGTCTATGACCTCTGAAAGCTATCAGATGTAAGCGGGCCTGGCCTGGGGGAAGGCGGGACGTTACATCCCG

Reverse complement sequence

CGGGATGTAACGTCCCGCCTTCCCCCAGGCCAGGCCCGCTTACATCTGATAGCTTTCAGAGGTCATAGACTGCCCTCACAGACCAACACATATCTTTTCT[GCACACTTTGTCCTCACTCATGTGCACCCGGGAAGATGTCCTCACTCGTGTGCACCCGGGAAGAATTTCCCGGTT/GCACACTTTGTCCTCACTCATGTGCACCCGGGAAGATGTCCTCACTCGTGTGCACCCGGGAAGAATTTCCCGGTC,T]
GGTCACCCATCCCAAATTGCTCCAGGCCAAGCACGCTTAACCCTGGAGTTCTTTGGAGATTGGATTCCGGAAAAGAAGTTGCAACTTGTTGATATGAGTA

Allele Frequencies:

Populations Population SizeFrequency of AACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC(primary allele) Frequency of GACCGGGAAATTCTTCCCGG GTGCACACGAGTGAGGACAT CTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.20% 1.80% 5.25% 1.74% A: 0.04%
All Indica  2759 86.80% 2.10% 8.26% 2.83% NA
All Japonica  1512 97.30% 1.50% 0.99% 0.07% A: 0.13%
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 76.10% 3.70% 15.13% 5.04% NA
Indica II  465 84.70% 2.20% 10.32% 2.80% NA
Indica III  913 92.00% 2.10% 4.60% 1.31% NA
Indica Intermediate  786 89.90% 1.00% 6.11% 2.93% NA
Temperate Japonica  767 99.30% 0.30% 0.39% 0.00% NA
Tropical Japonica  504 97.00% 0.20% 2.38% 0.00% A: 0.40%
Japonica Intermediate  241 91.30% 8.30% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 2.20% 3.33% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A LOC_Os01g31810.2 upstream_gene_variant ; 2330.0bp to feature; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A LOC_Os01g31820.1 upstream_gene_variant ; 1139.0bp to feature; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A LOC_Os01g31830.1 downstream_gene_variant ; 4051.0bp to feature; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> A LOC_Os01g31810-LOC_Os01g31820 intergenic_region ; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC LOC_Os01g31810.2 upstream_gene_variant ; 2329.0bp to feature; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC LOC_Os01g31820.1 upstream_gene_variant ; 1140.0bp to feature; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC LOC_Os01g31830.1 downstream_gene_variant ; 4052.0bp to feature; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> GACCGGGAAATTCTTCCCGGGTGCACACGA GTGAGGACATCTTCCCGGGTGCACATGAGT GAGGACAAAGTGTGC LOC_Os01g31810-LOC_Os01g31820 intergenic_region ; MODIFIER silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0117431722 AACCGGGAAATTCTTCCCGGGTGCACACGAGTGAGGACATCTTCCCGGGTGCACATGAGTGAGGACAAAGTGTGC -> DEL N N silent_mutation Average:28.834; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0117431722 9.71E-06 NA mr1613_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
vg0117431722 1.36E-08 NA mr1613_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