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Detailed information for vg1018676755:

Variant ID: vg1018676755 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 18676755
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATAAGATGCAACCAATAAATGGTAGATTTTTAAAGATTGATTTTAGAAGAATCTAGTTTAGCTACTGAGTAATGTACAAGAGCTTGCCAAAAGAAGCAA[C/A]
TACGTCTGAGCACATACATACAAAACTGTGGTATGTGAAATGTGATTGGAACAAAATATATATATATACTATATATAGGACACTCATATGGGGCACCATG

Reverse complement sequence

CATGGTGCCCCATATGAGTGTCCTATATATAGTATATATATATATTTTGTTCCAATCACATTTCACATACCACAGTTTTGTATGTATGTGCTCAGACGTA[G/T]
TTGCTTCTTTTGGCAAGCTCTTGTACATTACTCAGTAGCTAAACTAGATTCTTCTAAAATCAATCTTTAAAAATCTACCATTTATTGGTTGCATCTTATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.80% 1.20% 0.99% 0.00% NA
All Indica  2759 96.30% 2.00% 1.63% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.40% 6.40% 6.22% 0.00% NA
Indica II  465 98.70% 0.90% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 1.80% 0.76% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg1018676755 C -> A LOC_Os10g35010.1 intron_variant ; MODIFIER silent_mutation Average:35.708; most accessible tissue: Callus, score: 45.525 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018676755 6.35E-09 3.20E-19 mr1038 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
vg1018676755 2.34E-06 1.23E-12 mr1141 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
vg1018676755 1.37E-07 1.34E-19 mr1389 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
vg1018676755 3.84E-06 5.71E-17 mr1038_2 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
vg1018676755 NA 1.06E-14 mr1389_2 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