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Detailed information for vg1205884419:

Variant ID: vg1205884419 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 5884419
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTCATCATCAAACTGTACCTCCATCGACACTAGGTCGGCAACGATCTCCTTGAAGACCGATATGTGGTTCAACACAGAACCACTCTCCTGCAACTTGTG[T/C]
GAGAATAACTTCATCTTGATATGCATCTTACTGGTTAGATCTTTAGACATGCAGATCGATTCCAGTTTGAGCCAAAGTTCTTCAGCAGTCTTTTCCTGCA

Reverse complement sequence

TGCAGGAAAAGACTGCTGAAGAACTTTGGCTCAAACTGGAATCGATCTGCATGTCTAAAGATCTAACCAGTAAGATGCATATCAAGATGAAGTTATTCTC[A/G]
CACAAGTTGCAGGAGAGTGGTTCTGTGTTGAACCACATATCGGTCTTCAAGGAGATCGTTGCCGACCTAGTGTCGATGGAGGTACAGTTTGATGATGAAG

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 41.10% 12.50% 11.45% 34.96% NA
All Indica  2759 59.50% 4.00% 16.64% 19.83% NA
All Japonica  1512 5.80% 30.20% 1.39% 62.70% NA
Aus  269 62.50% 4.80% 20.07% 12.64% NA
Indica I  595 8.40% 11.10% 39.16% 41.34% NA
Indica II  465 78.10% 2.40% 9.03% 10.54% NA
Indica III  913 85.10% 0.30% 5.15% 9.42% NA
Indica Intermediate  786 57.50% 3.90% 17.43% 21.12% NA
Temperate Japonica  767 8.00% 38.60% 1.43% 52.02% NA
Tropical Japonica  504 4.20% 13.30% 1.39% 81.15% NA
Japonica Intermediate  241 2.10% 38.60% 1.24% 58.09% NA
VI/Aromatic  96 13.50% 0.00% 0.00% 86.46% NA
Intermediate  90 36.70% 11.10% 7.78% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1205884419 T -> C LOC_Os12g10890.1 synonymous_variant ; p.Ser110Ser; LOW synonymous_codon Average:12.431; most accessible tissue: Minghui63 root, score: 23.574 N N N N
vg1205884419 T -> DEL LOC_Os12g10890.1 N frameshift_variant Average:12.431; most accessible tissue: Minghui63 root, score: 23.574 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205884419 4.23E-06 NA mr1619 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