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Detailed information for vg0719604554:

Variant ID: vg0719604554 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19604554
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATGCAAAATTCTCAGTCGAACAGAGCCTTAGTGGTGGCGGAGCCAAAAGCTTTTGGAAGTTTGACCAATGAGATAGCTCCAATTATCAGGGGCGGGCC[C/T]
AGGATTTGAAGGTTGGGTATTCAAAATAAAGAGGGGGAAAATTTTCTACACTCAAAAATCATAATAATTGGTTTATATAATATCACATACTAGTAGTTAT

Reverse complement sequence

ATAACTACTAGTATGTGATATTATATAAACCAATTATTATGATTTTTGAGTGTAGAAAATTTTCCCCCTCTTTATTTTGAATACCCAACCTTCAAATCCT[G/A]
GGCCCGCCCCTGATAATTGGAGCTATCTCATTGGTCAAACTTCCAAAAGCTTTTGGCTCCGCCACCACTAAGGCTCTGTTCGACTGAGAATTTTGCATGA

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 92.00% 7.80% 0.19% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 75.40% 24.00% 0.60% 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 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 57.50% 41.30% 1.17% 0.00% NA
Tropical Japonica  504 96.20% 3.80% 0.00% 0.00% NA
Japonica Intermediate  241 88.80% 11.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0719604554 C -> T LOC_Os07g32774.2 upstream_gene_variant ; 1714.0bp to feature; MODIFIER silent_mutation Average:25.181; most accessible tissue: Callus, score: 43.662 N N N N
vg0719604554 C -> T LOC_Os07g32774.1 intron_variant ; MODIFIER silent_mutation Average:25.181; most accessible tissue: Callus, score: 43.662 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719604554 2.63E-06 NA mr1163 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
vg0719604554 6.90E-06 NA mr1757 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