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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0109361051:

Variant ID: vg0109361051 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 9361051
Reference Allele: CAlternative Allele: CGCAGACCCCTTCGTGTA,CGCAGACCCCTTCGTG,CGCAGACCCCTTCG,CGCAGACCCCT,CGCAGACCCCTTCGTGTATG,T
Primary Allele: CSecondary Allele: CGCAGACCCCTTCGTGTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCGTTGTACCATGTCGCAAGCGTCTTTGAGGGTGGTTCGCTAGAAAAATCCTTGTCGAAAAGCTTTTCCGACTAGTGTACGACCGGAGGCATGTGACC[C/CGCAGACCCCTTCGTGTA,CGCAGACCCCTTCGTG,CGCAGACCCCTTCG,CGCAGACCCCT,CGCAGACCCCTTCGTGTATG,T]
TGACGGAGCGTGGGGCTCCTCACCGGGAGACCGCGCTGGCCCCCCTTTGCCGGTTCGGCCGGGGACCCTGGGTGAGACTCTAAGCTCCCAATCTGTGGAA

Reverse complement sequence

TTCCACAGATTGGGAGCTTAGAGTCTCACCCAGGGTCCCCGGCCGAACCGGCAAAGGGGGGCCAGCGCGGTCTCCCGGTGAGGAGCCCCACGCTCCGTCA[G/TACACGAAGGGGTCTGCG,CACGAAGGGGTCTGCG,CGAAGGGGTCTGCG,AGGGGTCTGCG,CATACACGAAGGGGTCTGCG,A]
GGTCACATGCCTCCGGTCGTACACTAGTCGGAAAAGCTTTTCGACAAGGATTTTTCTAGCGAACCACCCTCAAAGACGCTTGCGACATGGTACAACGGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CGCAGACCCCTTCGTGTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.70% 7.80% 39.42% 10.26% CGCAGACCCCTTCG: 3.66%; T: 2.20%; CGCAGACCCCT: 1.61%; CGCAGACCCCTTCGTGTATG: 1.44%; CGCAGACCCCTTCGTG: 0.91%
All Indica  2759 3.50% 12.50% 57.77% 14.14% CGCAGACCCCTTCG: 5.84%; CGCAGACCCCT: 2.32%; CGCAGACCCCTTCGTGTATG: 2.28%; CGCAGACCCCTTCGTG: 1.52%; T: 0.18%
All Japonica  1512 86.50% 0.60% 5.82% 0.07% T: 6.28%; CGCAGACCCCTTCG: 0.40%; CGCAGACCCCT: 0.13%; CGCAGACCCCTTCGTGTATG: 0.13%; CGCAGACCCCTTCGTG: 0.07%
Aus  269 5.20% 4.80% 52.79% 33.09% CGCAGACCCCT: 3.35%; CGCAGACCCCTTCG: 0.37%; CGCAGACCCCTTCGTGTATG: 0.37%
Indica I  595 5.50% 6.60% 76.81% 4.71% CGCAGACCCCTTCGTGTATG: 2.52%; CGCAGACCCCTTCG: 2.18%; CGCAGACCCCT: 1.01%; CGCAGACCCCTTCGTG: 0.67%
Indica II  465 2.80% 11.00% 52.26% 23.44% CGCAGACCCCTTCG: 4.09%; CGCAGACCCCT: 3.01%; CGCAGACCCCTTCGTGTATG: 1.72%; CGCAGACCCCTTCGTG: 1.29%; T: 0.43%
Indica III  913 1.80% 17.70% 46.00% 16.76% CGCAGACCCCTTCG: 9.09%; CGCAGACCCCT: 3.18%; CGCAGACCCCTTCGTGTATG: 3.18%; CGCAGACCCCTTCGTG: 2.30%
Indica Intermediate  786 4.30% 11.70% 60.31% 12.72% CGCAGACCCCTTCG: 5.85%; CGCAGACCCCT: 1.91%; CGCAGACCCCTTCGTG: 1.40%; CGCAGACCCCTTCGTGTATG: 1.40%; T: 0.38%
Temperate Japonica  767 95.00% 0.10% 2.48% 0.00% T: 2.09%; CGCAGACCCCTTCG: 0.13%; CGCAGACCCCTTCGTG: 0.13%
Tropical Japonica  504 77.60% 1.20% 9.52% 0.00% T: 11.11%; CGCAGACCCCTTCGTGTATG: 0.40%; CGCAGACCCCT: 0.20%
Japonica Intermediate  241 78.00% 0.80% 8.71% 0.41% T: 9.54%; CGCAGACCCCTTCG: 2.07%; CGCAGACCCCT: 0.41%
VI/Aromatic  96 87.50% 1.00% 7.29% 1.04% CGCAGACCCCTTCG: 3.12%
Intermediate  90 47.80% 2.20% 35.56% 4.44% T: 4.44%; CGCAGACCCCTTCG: 2.22%; CGCAGACCCCTTCGTGTATG: 2.22%; CGCAGACCCCT: 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
vg0109361051 C -> CGCAGACCCCTTCGTGTATG LOC_Os01g16480.1 downstream_gene_variant ; 1652.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTGTATG LOC_Os01g16490.1 downstream_gene_variant ; 301.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTGTATG LOC_Os01g16500.1 downstream_gene_variant ; 2694.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTGTATG LOC_Os01g16480-LOC_Os01g16490 intergenic_region ; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> T LOC_Os01g16480.1 downstream_gene_variant ; 1651.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> T LOC_Os01g16490.1 downstream_gene_variant ; 302.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> T LOC_Os01g16500.1 downstream_gene_variant ; 2695.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> T LOC_Os01g16480-LOC_Os01g16490 intergenic_region ; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCG LOC_Os01g16480.1 downstream_gene_variant ; 1652.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCG LOC_Os01g16490.1 downstream_gene_variant ; 301.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCG LOC_Os01g16500.1 downstream_gene_variant ; 2694.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCG LOC_Os01g16480-LOC_Os01g16490 intergenic_region ; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTGTA LOC_Os01g16480.1 downstream_gene_variant ; 1652.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTGTA LOC_Os01g16490.1 downstream_gene_variant ; 301.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTGTA LOC_Os01g16500.1 downstream_gene_variant ; 2694.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTGTA LOC_Os01g16480-LOC_Os01g16490 intergenic_region ; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTG LOC_Os01g16480.1 downstream_gene_variant ; 1652.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTG LOC_Os01g16490.1 downstream_gene_variant ; 301.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTG LOC_Os01g16500.1 downstream_gene_variant ; 2694.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCTTCGTG LOC_Os01g16480-LOC_Os01g16490 intergenic_region ; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> DEL N N silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCT LOC_Os01g16480.1 downstream_gene_variant ; 1652.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCT LOC_Os01g16490.1 downstream_gene_variant ; 301.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCT LOC_Os01g16500.1 downstream_gene_variant ; 2694.0bp to feature; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0109361051 C -> CGCAGACCCCT LOC_Os01g16480-LOC_Os01g16490 intergenic_region ; MODIFIER silent_mutation Average:33.964; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109361051 9.70E-06 9.70E-06 mr1085 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
vg0109361051 NA 2.51E-06 mr1104 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
vg0109361051 NA 3.81E-08 mr1213 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
vg0109361051 NA 2.63E-12 mr1410 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
vg0109361051 NA 5.70E-06 mr1104_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
vg0109361051 NA 1.14E-11 mr1410_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