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Detailed information for vg1201300655:

Variant ID: vg1201300655 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 1300655
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTTTCCGCCTTTGCCTCCGCCTTGGTGTCCGCCATCACGAAGGCGAAGGCTCCACCACCGAACTCCTCCCCCTCGCGAACAAGCTAATCCCCCGAAGA[A/C]
ACTTGTACTTCTTGGCCGGCCAAGATCGAACCAATCCTAAATCCCCCCCTAAAAAAGGCGAGAAAATCAGGAATTTGGAGGCGAGAGATTGAAGCTTGGG

Reverse complement sequence

CCCAAGCTTCAATCTCTCGCCTCCAAATTCCTGATTTTCTCGCCTTTTTTAGGGGGGGATTTAGGATTGGTTCGATCTTGGCCGGCCAAGAAGTACAAGT[T/G]
TCTTCGGGGGATTAGCTTGTTCGCGAGGGGGAGGAGTTCGGTGGTGGAGCCTTCGCCTTCGTGATGGCGGACACCAAGGCGGAGGCAAAGGCGGAAACTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.30% 16.70% 0.04% 0.00% NA
All Indica  2759 81.60% 18.40% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 1.90% 98.10% 0.00% 0.00% NA
Indica I  595 97.10% 2.90% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 63.20% 36.80% 0.00% 0.00% NA
Indica Intermediate  786 82.40% 17.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 93.80% 5.20% 1.04% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1201300655 A -> C LOC_Os12g03340.1 5_prime_UTR_variant ; 64.0bp to feature; MODIFIER silent_mutation Average:75.318; most accessible tissue: Minghui63 root, score: 84.918 N N N N
vg1201300655 A -> C LOC_Os12g03360.1 upstream_gene_variant ; 4484.0bp to feature; MODIFIER silent_mutation Average:75.318; most accessible tissue: Minghui63 root, score: 84.918 N N N N
vg1201300655 A -> C LOC_Os12g03350.1 downstream_gene_variant ; 1685.0bp to feature; MODIFIER silent_mutation Average:75.318; most accessible tissue: Minghui63 root, score: 84.918 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1201300655 NA 1.39E-06 mr1063 Ind_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
vg1201300655 5.63E-06 NA mr1261 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
vg1201300655 2.26E-08 5.73E-11 mr1261 Ind_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
vg1201300655 NA 1.62E-06 mr1808 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
vg1201300655 NA 4.28E-21 mr1305_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