My apologies for omitting a line last time. I fed this to R --vanilla CMD BATCH and the behavior remains as it was. One might suppose that 3' UTR variants are a subset of AllVariants()...? ## code and sessionInfo() below library(Homo.sapiens) library(VariantAnnotation) EIF2C3 <- org.Hs.egSYMBOL2EG[['EIF2C3']] ## [1] "192669" EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1)) EIF2C3.site %over% transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)[[EIF2C3]] ## TRUE allVars <- locateVariants(EIF2C3.site, TxDb.Hsapiens.UCSC.hg19.knownGene, AllVariants()) length(allVars) ## 0 threePrimeVars <- locateVariants(EIF2C3.site, TxDb.Hsapiens.UCSC.hg19.knownGene, ThreeUTRVariants()) length(threePrimeVars) ## 2 #R Under development (unstable) (2013-02-13 r61937) #Platform: x86_64-unknown-linux-gnu (64-bit) #locale: #[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 #[7] LC_PAPER=C LC_NAME=C #[9] LC_ADDRESS=C LC_TELEPHONE=C #[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C #attached base packages: #[1] parallel stats graphics grDevices utils datasets methods #[8] base #other attached packages: #[1] VariantAnnotation_1.5.36 #[2] Rsamtools_1.11.16 #[3] Biostrings_2.27.11 #[4] Homo.sapiens_1.0.0 #[5] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 #[6] org.Hs.eg.db_2.8.0 #[7] GO.db_2.8.0 #[8] RSQLite_0.11.2 #[9] DBI_0.2-5 #[10] OrganismDbi_1.1.13 #[11] GenomicFeatures_1.11.8 #[12] GenomicRanges_1.11.29 #[13] IRanges_1.17.32 #[14] AnnotationDbi_1.21.10 #[15] Biobase_2.19.2 #[16] BiocGenerics_0.5.6 #loaded via a namespace (and not attached): #[1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 graph_1.37.5 #[5] RBGL_1.35.0 RCurl_1.95-3 rtracklayer_1.19.9 stats4_3.0.0 #[9] tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0 proc.time() ## user system elapsed ## 26.397 0.472 27.247 Thanks for any insight. I'll also look to see if I can determine the cause. -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]