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Detailed information for vg0334873774:

Variant ID: vg0334873774 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 34873774
Reference Allele: GAAlternative Allele: G,GAA,AA,GAAA
Primary Allele: GASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAATAATTTATCTGGACAGCTCTTCACACTCACTACCTCCGTCTCAAAATAAGCTTATTTGTGAGTTTTTATGTTCAACATTTGACCGTCCGTCTTATTT[GA/G,GAA,AA,GAAA]
AAAAAAAAAGTAAAATAAGTCACGCGTAAAGTACTATTCATATTTTATCATCTAATAACAATAAAAATACTAATCATAAAAAAATTAAATAAAATGAATT

Reverse complement sequence

AATTCATTTTATTTAATTTTTTTATGATTAGTATTTTTATTGTTATTAGATGATAAAATATGAATAGTACTTTACGCGTGACTTATTTTACTTTTTTTTT[TC/C,TTC,TT,TTTC]
AAATAAGACGGACGGTCAAATGTTGAACATAAAAACTCACAAATAAGCTTATTTTGAGACGGAGGTAGTGAGTGTGAAGAGCTGTCCAGATAAATTATTA

Allele Frequencies:

Populations Population SizeFrequency of GA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.60% 3.10% 3.51% 20.14% AA: 2.07%; GAA: 1.38%; GAAA: 0.15%
All Indica  2759 60.30% 2.90% 1.41% 33.74% AA: 1.38%; GAA: 0.18%; GAAA: 0.04%
All Japonica  1512 85.50% 4.20% 6.15% 0.33% AA: 3.84%
Aus  269 65.40% 0.40% 10.41% 0.00% GAA: 21.19%; GAAA: 2.23%; AA: 0.37%
Indica I  595 78.80% 5.70% 1.18% 13.95% AA: 0.34%
Indica II  465 41.30% 2.60% 1.94% 54.19% NA
Indica III  913 60.80% 0.20% 0.66% 37.24% AA: 1.10%
Indica Intermediate  786 57.00% 4.20% 2.16% 32.57% AA: 3.31%; GAA: 0.64%; GAAA: 0.13%
Temperate Japonica  767 83.20% 6.50% 9.13% 0.26% AA: 0.91%
Tropical Japonica  504 93.10% 1.00% 1.98% 0.60% AA: 3.37%
Japonica Intermediate  241 77.20% 3.30% 5.39% 0.00% AA: 14.11%
VI/Aromatic  96 97.90% 0.00% 0.00% 0.00% GAA: 2.08%
Intermediate  90 70.00% 3.30% 6.67% 17.78% AA: 1.11%; GAA: 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
vg0334873774 GA -> GAA LOC_Os03g61470.1 upstream_gene_variant ; 2422.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> GAA LOC_Os03g61480.1 downstream_gene_variant ; 134.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> GAA LOC_Os03g61490.1 downstream_gene_variant ; 4267.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> GAA LOC_Os03g61470-LOC_Os03g61480 intergenic_region ; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> DEL N N silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> G LOC_Os03g61470.1 upstream_gene_variant ; 2421.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> G LOC_Os03g61480.1 downstream_gene_variant ; 135.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> G LOC_Os03g61490.1 downstream_gene_variant ; 4268.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> G LOC_Os03g61470-LOC_Os03g61480 intergenic_region ; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> AA LOC_Os03g61470.1 upstream_gene_variant ; 2420.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> AA LOC_Os03g61480.1 downstream_gene_variant ; 136.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> AA LOC_Os03g61490.1 downstream_gene_variant ; 4269.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> AA LOC_Os03g61470-LOC_Os03g61480 intergenic_region ; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> GAAA LOC_Os03g61470.1 upstream_gene_variant ; 2422.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> GAAA LOC_Os03g61480.1 downstream_gene_variant ; 134.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> GAAA LOC_Os03g61490.1 downstream_gene_variant ; 4267.0bp to feature; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0334873774 GA -> GAAA LOC_Os03g61470-LOC_Os03g61480 intergenic_region ; MODIFIER silent_mutation Average:44.301; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334873774 7.65E-06 7.45E-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
vg0334873774 NA 2.58E-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
vg0334873774 1.30E-06 1.18E-09 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
vg0334873774 NA 3.15E-07 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
vg0334873774 NA 8.28E-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
vg0334873774 NA 6.64E-07 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
vg0334873774 NA 1.44E-07 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
vg0334873774 NA 1.56E-06 mr1247 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
vg0334873774 4.50E-06 9.48E-09 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
vg0334873774 NA 8.50E-07 mr1691 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
vg0334873774 8.40E-07 3.37E-12 mr1693 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
vg0334873774 NA 3.89E-06 mr1917 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
vg0334873774 NA 3.08E-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
vg0334873774 4.89E-06 1.35E-09 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
vg0334873774 NA 2.07E-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
vg0334873774 NA 7.51E-07 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
vg0334873774 NA 2.93E-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
vg0334873774 NA 1.73E-07 mr1180_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
vg0334873774 NA 6.09E-08 mr1183_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
vg0334873774 NA 2.44E-06 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
vg0334873774 NA 3.44E-07 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
vg0334873774 NA 9.49E-07 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
vg0334873774 5.98E-06 2.42E-10 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
vg0334873774 NA 4.15E-08 mr1691_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
vg0334873774 NA 5.09E-07 mr1720_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
vg0334873774 NA 5.10E-06 mr1936_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