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Detailed information for vg1117271234:

Variant ID: vg1117271234 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 17271234
Reference Allele: TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAAAlternative Allele: T,ATTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA
Primary Allele: TTTTGGCATTGCCAAAATTT TGGCATAGTTGCCAAAATTT TGGCAGGATTTCTTATATAG CTACCAAAASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGAAGTGAAGAGAAGAATATGCTAGTGGTATTTTCTTTGTTGTACAATTTTAAACAAAAGGGCTGTTCACTTTGTTGCCAAAAAAAAACCTTACCAAA[TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA/T,ATTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA]
TTTGGCAGCAAACTAAATGTAGCTACTTTTTTGGCAACTTTACTAAAATTTGGTAAGATTAAAAATGGCACCAAAGTGAACAGGCCCAAAGAATCTAGTA

Reverse complement sequence

TACTAGATTCTTTGGGCCTGTTCACTTTGGTGCCATTTTTAATCTTACCAAATTTTAGTAAAGTTGCCAAAAAAGTAGCTACATTTAGTTTGCTGCCAAA[TTTTGGTAGCTATATAAGAAATCCTGCCAAAATTTTGGCAACTATGCCAAAATTTTGGCAATGCCAAAA/A,TTTTGGTAGCTATATAAGAAATCCTGCCAAAATTTTGGCAACTATGCCAAAATTTTGGCAATGCCAAAT]
TTTGGTAAGGTTTTTTTTTGGCAACAAAGTGAACAGCCCTTTTGTTTAAAATTGTACAACAAAGAAAATACCACTAGCATATTCTTCTCTTCACTTCACC

Allele Frequencies:

Populations Population SizeFrequency of TTTTGGCATTGCCAAAATTT TGGCATAGTTGCCAAAATTT TGGCAGGATTTCTTATATAG CTACCAAAA(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.70% 1.10% 1.04% 10.14% NA
All Indica  2759 87.10% 1.90% 0.54% 10.40% NA
All Japonica  1512 87.90% 0.10% 2.18% 9.85% NA
Aus  269 89.20% 0.00% 0.37% 10.41% NA
Indica I  595 92.60% 2.50% 0.84% 4.03% NA
Indica II  465 85.40% 3.00% 0.65% 10.97% NA
Indica III  913 84.20% 0.70% 0.22% 14.90% NA
Indica Intermediate  786 87.40% 2.30% 0.64% 9.67% NA
Temperate Japonica  767 91.50% 0.00% 2.22% 6.26% NA
Tropical Japonica  504 89.90% 0.20% 1.59% 8.33% NA
Japonica Intermediate  241 72.20% 0.00% 3.32% 24.48% NA
VI/Aromatic  96 89.60% 0.00% 0.00% 10.42% NA
Intermediate  90 94.40% 0.00% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117271234 TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA -> ATTTGGCATTGCCAAAATTTTGGCATAGTT GCCAAAATTTTGGCAGGATTTCTTATATAG CTACCAAAA LOC_Os11g29760.1 downstream_gene_variant ; 1942.0bp to feature; MODIFIER N Average:43.126; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg1117271234 TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA -> ATTTGGCATTGCCAAAATTTTGGCATAGTT GCCAAAATTTTGGCAGGATTTCTTATATAG CTACCAAAA LOC_Os11g29770.1 downstream_gene_variant ; 2099.0bp to feature; MODIFIER N Average:43.126; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg1117271234 TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA -> ATTTGGCATTGCCAAAATTTTGGCATAGTT GCCAAAATTTTGGCAGGATTTCTTATATAG CTACCAAAA LOC_Os11g29760-LOC_Os11g29770 intergenic_region ; MODIFIER N Average:43.126; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg1117271234 TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA -> T LOC_Os11g29760.1 downstream_gene_variant ; 1943.0bp to feature; MODIFIER silent_mutation Average:43.126; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg1117271234 TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA -> T LOC_Os11g29770.1 downstream_gene_variant ; 2098.0bp to feature; MODIFIER silent_mutation Average:43.126; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg1117271234 TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA -> T LOC_Os11g29760-LOC_Os11g29770 intergenic_region ; MODIFIER silent_mutation Average:43.126; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N
vg1117271234 TTTTGGCATTGCCAAAATTTTGGCATAGTTGCCAAAATTTTGGCAGGATTTCTTATATAGCTACCAAAA -> DEL N N silent_mutation Average:43.126; most accessible tissue: Minghui63 flag leaf, score: 75.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117271234 NA 2.52E-07 mr1350_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
vg1117271234 1.36E-06 1.36E-06 mr1542_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