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Detailed information for vg1001300112:

Variant ID: vg1001300112 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1300112
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCTAAGCATGACTAAGCATCTATAATAATCATATAGCTGAACCAAACCAATATATAAGGTTCTAGCTAATCAAATTATAACCCATAGGAAAATAAAGT[T/C]
ATCTTCGGCCATAATTAAATGGGAAAGGCTCACCACCCGGTGACATTCGAAAATAATGTATAAGTTCAAATAAAACATTAGCTTTAAACGGGTTCAACAT

Reverse complement sequence

ATGTTGAACCCGTTTAAAGCTAATGTTTTATTTGAACTTATACATTATTTTCGAATGTCACCGGGTGGTGAGCCTTTCCCATTTAATTATGGCCGAAGAT[A/G]
ACTTTATTTTCCTATGGGTTATAATTTGATTAGCTAGAACCTTATATATTGGTTTGGTTCAGCTATATGATTATTATAGATGCTTAGTCATGCTTAGAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.70% 21.40% 14.92% 16.04% NA
All Indica  2759 65.60% 4.20% 21.24% 8.92% NA
All Japonica  1512 8.50% 56.10% 5.03% 30.36% NA
Aus  269 93.30% 1.50% 1.49% 3.72% NA
Indica I  595 66.40% 9.70% 10.59% 13.28% NA
Indica II  465 50.10% 4.70% 34.84% 10.32% NA
Indica III  913 68.90% 1.50% 23.44% 6.13% NA
Indica Intermediate  786 70.40% 2.90% 18.70% 8.02% NA
Temperate Japonica  767 1.30% 85.40% 3.13% 10.17% NA
Tropical Japonica  504 20.40% 20.00% 5.75% 53.77% NA
Japonica Intermediate  241 6.60% 38.20% 9.54% 45.64% NA
VI/Aromatic  96 20.80% 20.80% 23.96% 34.38% NA
Intermediate  90 47.80% 23.30% 17.78% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001300112 T -> C LOC_Os10g03090.1 upstream_gene_variant ; 877.0bp to feature; MODIFIER silent_mutation Average:32.035; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg1001300112 T -> C LOC_Os10g03080-LOC_Os10g03090 intergenic_region ; MODIFIER silent_mutation Average:32.035; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg1001300112 T -> DEL N N silent_mutation Average:32.035; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001300112 NA 6.96E-06 mr1179 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
vg1001300112 5.71E-06 1.05E-08 mr1205 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
vg1001300112 NA 1.52E-07 mr1206 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
vg1001300112 NA 5.85E-07 mr1403 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
vg1001300112 NA 5.43E-09 mr1570 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
vg1001300112 NA 1.69E-07 mr1723 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