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Detailed information for vg1101320463:

Variant ID: vg1101320463 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1320463
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATTAAAATTTAAGTTTGGCTGTGAGTGATAAGCTGAAGAGAAAAATATGATTTGAACACACTTGTAGCTAGCTGAGTAAGGTTTAGAGACATATAAAA[T/C]
CCCAATGCAATATATAATCAGGTTAGTCCTTTTATGCGGGTTTGTTCGGAGGACATATTGACAGTTGTAACTTCTCCCAAAATCAGAAACTCACAGTATA

Reverse complement sequence

TATACTGTGAGTTTCTGATTTTGGGAGAAGTTACAACTGTCAATATGTCCTCCGAACAAACCCGCATAAAAGGACTAACCTGATTATATATTGCATTGGG[A/G]
TTTTATATGTCTCTAAACCTTACTCAGCTAGCTACAAGTGTGTTCAAATCATATTTTTCTCTTCAGCTTATCACTCACAGCCAAACTTAAATTTTAATAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.80% 1.10% 0.15% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 96.60% 3.00% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 95.80% 3.50% 0.65% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1101320463 T -> C LOC_Os11g03440.1 upstream_gene_variant ; 1758.0bp to feature; MODIFIER silent_mutation Average:29.125; most accessible tissue: Callus, score: 70.183 N N N N
vg1101320463 T -> C LOC_Os11g03450.1 upstream_gene_variant ; 4156.0bp to feature; MODIFIER silent_mutation Average:29.125; most accessible tissue: Callus, score: 70.183 N N N N
vg1101320463 T -> C LOC_Os11g03460.1 downstream_gene_variant ; 4996.0bp to feature; MODIFIER silent_mutation Average:29.125; most accessible tissue: Callus, score: 70.183 N N N N
vg1101320463 T -> C LOC_Os11g03440-LOC_Os11g03450 intergenic_region ; MODIFIER silent_mutation Average:29.125; most accessible tissue: Callus, score: 70.183 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1101320463 NA 6.67E-06 mr1100 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
vg1101320463 2.65E-06 2.65E-06 mr1609 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
vg1101320463 NA 2.42E-06 mr1613 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
vg1101320463 NA 7.90E-06 mr1989 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