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Detailed information for vg1205788235:

Variant ID: vg1205788235 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 5788235
Reference Allele: TTAAlternative Allele: CTA,T
Primary Allele: TTASecondary Allele: CTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCCTTTTTTTTGGAACTTTGTAACTCTTATTCCTTCAATTGTTCCACTGTTCTCTTGTGGCATTTTTTTCTAAAATACCGATAATAAATGTCTCAAGA[TTA/CTA,T]
TGTTTTATCTGACAGTTTATTAAATGCCTCTAATAAATGCCATTAGACTCCACTCAAGTTGTTTTCAGAGGCATAGTACAAAATGCATGCCTCTACTATA

Reverse complement sequence

TATAGTAGAGGCATGCATTTTGTACTATGCCTCTGAAAACAACTTGAGTGGAGTCTAATGGCATTTATTAGAGGCATTTAATAAACTGTCAGATAAAACA[TAA/TAG,A]
TCTTGAGACATTTATTATCGGTATTTTAGAAAAAAATGCCACAAGAGAACAGTGGAACAATTGAAGGAATAAGAGTTACAAAGTTCCAAAAAAAAGGAAT

Allele Frequencies:

Populations Population SizeFrequency of TTA(primary allele) Frequency of CTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.30% 8.40% 1.23% 0.00% T: 0.08%
All Indica  2759 99.20% 0.60% 0.14% 0.00% T: 0.07%
All Japonica  1512 72.80% 23.80% 3.37% 0.00% NA
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 98.70% 1.10% 0.00% 0.00% T: 0.22%
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 98.90% 0.80% 0.25% 0.00% T: 0.13%
Temperate Japonica  767 55.70% 38.70% 5.61% 0.00% NA
Tropical Japonica  504 95.20% 4.00% 0.79% 0.00% NA
Japonica Intermediate  241 80.50% 17.80% 1.66% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 82.20% 14.40% 1.11% 0.00% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1205788235 TTA -> CTA LOC_Os12g10760.1 upstream_gene_variant ; 1666.0bp to feature; MODIFIER silent_mutation Average:50.796; most accessible tissue: Callus, score: 82.325 N N N N
vg1205788235 TTA -> CTA LOC_Os12g10770.1 upstream_gene_variant ; 4786.0bp to feature; MODIFIER silent_mutation Average:50.796; most accessible tissue: Callus, score: 82.325 N N N N
vg1205788235 TTA -> CTA LOC_Os12g10760-LOC_Os12g10770 intergenic_region ; MODIFIER silent_mutation Average:50.796; most accessible tissue: Callus, score: 82.325 N N N N
vg1205788235 TTA -> T LOC_Os12g10760.1 upstream_gene_variant ; 1667.0bp to feature; MODIFIER silent_mutation Average:50.796; most accessible tissue: Callus, score: 82.325 N N N N
vg1205788235 TTA -> T LOC_Os12g10770.1 upstream_gene_variant ; 4785.0bp to feature; MODIFIER silent_mutation Average:50.796; most accessible tissue: Callus, score: 82.325 N N N N
vg1205788235 TTA -> T LOC_Os12g10760-LOC_Os12g10770 intergenic_region ; MODIFIER silent_mutation Average:50.796; most accessible tissue: Callus, score: 82.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205788235 7.26E-06 7.26E-06 mr1260 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
vg1205788235 NA 8.13E-06 mr1708 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
vg1205788235 4.33E-06 4.31E-06 mr1736 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
vg1205788235 NA 8.88E-07 mr1803 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
vg1205788235 NA 3.29E-06 mr1577_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
vg1205788235 NA 3.95E-06 mr1966_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