chrM is the broken old hg19 mitogenome chrMT is rCRS, same as hg38 chrM
--t > On Oct 12, 2025, at 12:30 PM, Raymond Cavalcante <[email protected]> wrote: > > Hi, > > I was testing the annotatr package after fixing the ggplot2 v4 stuff, but I > got an error in my vignette build and discovered what I think is an error > in the result of Seqinfo::seqinfo(genome = 'hg19'). > > There are two mitochondrial chromosomes for hg19. This causes some > downstream issues when merging hg19 GRanges. > >> Seqinfo::Seqinfo(genome='hg19')[c('chrM', 'chrMT')] > Seqinfo object with 2 sequences (2 circular) from hg19 genome: > seqnames seqlengths isCircular genome > chrM 16571 TRUE hg19 > chrMT 16569 TRUE hg19 > > I checked hg38 on a lark and it appears correct. > >> Seqinfo::Seqinfo(genome='hg38')[c('chrM', 'chrMT')] > Seqinfo object with 2 sequences (1 circular) from 2 genomes (hg38, NA): > seqnames seqlengths isCircular genome > chrM 16569 TRUE hg38 > chrMT NA NA <NA> > > I'm using 0.99.2 of Seqinfo in a Bioconductor devel Docker image. > > My session info: > >> devtools::session_info() > ─ Session info > ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── > setting value > version R version 4.5.1 (2025-06-13) > os Ubuntu 24.04.3 LTS > system x86_64, linux-gnu > ui X11 > language (EN) > collate en_US.UTF-8 > ctype en_US.UTF-8 > tz Etc/UTC > date 2025-10-12 > pandoc 3.8.1 @ /usr/bin/pandoc > quarto 1.7.32 @ /usr/local/bin/quarto > > ─ Packages > ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── > ! package * version date (UTC) lib source > abind 1.4-8 2024-09-12 [1] RSPM (R > 4.5.0) > AnnotationDbi * 1.71.1 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > AnnotationHub 3.99.6 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > VP annotatr * 1.35.1 2025-05-13 [?] > Bioconductor 3.22 (R 4.5.0) (on disk 1.35.0) > Biobase * 2.69.1 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > BiocFileCache 2.99.6 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > BiocGenerics * 0.55.3 2025-10-09 [1] > Bioconductor 3.22 (R 4.5.1) > BiocIO 1.19.0 2025-04-15 [1] > Bioconductor 3.22 (R 4.5.0) > BiocManager 1.30.26 2025-06-05 [1] CRAN (R > 4.5.1) > BiocParallel 1.43.4 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > BiocVersion 3.22.0 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > Biostrings 2.77.2 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > bit 4.6.0 2025-03-06 [1] RSPM (R > 4.5.0) > bit64 4.6.0-1 2025-01-16 [1] RSPM (R > 4.5.0) > bitops 1.0-9 2024-10-03 [1] RSPM (R > 4.5.0) > blob 1.2.4 2023-03-17 [1] RSPM (R > 4.5.0) > brio 1.1.5 2024-04-24 [1] RSPM (R > 4.5.0) > BSgenome 1.77.2 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > cachem 1.1.0 2024-05-16 [1] RSPM (R > 4.5.0) > cli 3.6.5 2025-04-23 [1] RSPM (R > 4.5.0) > codetools 0.2-20 2024-03-31 [2] CRAN (R > 4.5.1) > crayon 1.5.3 2024-06-20 [1] RSPM (R > 4.5.0) > curl 7.0.0 2025-08-19 [1] RSPM (R > 4.5.0) > DBI 1.2.3 2024-06-02 [1] RSPM (R > 4.5.0) > dbplyr 2.5.1 2025-09-10 [1] RSPM (R > 4.5.0) > DelayedArray 0.35.3 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > desc 1.4.3 2023-12-10 [1] RSPM (R > 4.5.0) > devtools 2.4.6 2025-10-03 [1] RSPM (R > 4.5.0) > dplyr 1.1.4 2023-11-17 [1] RSPM (R > 4.5.0) > ellipsis 0.3.2 2021-04-29 [1] RSPM (R > 4.5.0) > farver 2.1.2 2024-05-13 [1] RSPM (R > 4.5.0) > fastmap 1.2.0 2024-05-15 [1] RSPM (R > 4.5.0) > filelock 1.0.3 2023-12-11 [1] RSPM (R > 4.5.0) > fs 1.6.6 2025-04-12 [1] RSPM (R > 4.5.0) > generics * 0.1.4 2025-05-09 [1] RSPM (R > 4.5.0) > GenomeInfoDb 1.45.12 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > GenomicAlignments 1.45.4 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > GenomicFeatures * 1.61.6 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > GenomicRanges * 1.61.5 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > ggplot2 4.0.0 2025-09-11 [1] RSPM (R > 4.5.0) > glue 1.8.0 2024-09-30 [1] RSPM (R > 4.5.0) > gtable 0.3.6 2024-10-25 [1] RSPM (R > 4.5.0) > hms 1.1.3 2023-03-21 [1] RSPM (R > 4.5.0) > httr 1.4.7 2023-08-15 [1] RSPM (R > 4.5.0) > httr2 1.2.1 2025-07-22 [1] RSPM (R > 4.5.0) > IRanges * 2.43.5 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > jsonlite 2.0.0 2025-03-27 [1] RSPM (R > 4.5.0) > KEGGREST 1.49.2 2025-10-10 [1] > Bioconductor 3.22 (R 4.5.1) > lattice 0.22-7 2025-04-02 [2] CRAN (R > 4.5.1) > lifecycle 1.0.4 2023-11-07 [1] RSPM (R > 4.5.0) > magrittr 2.0.4 2025-09-12 [1] RSPM (R > 4.5.0) > Matrix 1.7-4 2025-08-28 [1] RSPM (R > 4.5.0) > MatrixGenerics 1.21.0 2025-04-15 [1] > Bioconductor 3.22 (R 4.5.0) > matrixStats 1.5.0 2025-01-07 [1] RSPM (R > 4.5.0) > memoise 2.0.1 2021-11-26 [1] RSPM (R > 4.5.0) > org.Hs.eg.db * 3.22.0 2025-10-11 [1] > Bioconductor > pillar 1.11.1 2025-09-17 [1] RSPM (R > 4.5.0) > pkgbuild 1.4.8 2025-05-26 [1] RSPM (R > 4.5.0) > pkgconfig 2.0.3 2019-09-22 [1] RSPM (R > 4.5.0) > pkgload 1.4.1 2025-09-23 [1] RSPM (R > 4.5.0) > plyr 1.8.9 2023-10-02 [1] RSPM (R > 4.5.0) > png 0.1-8 2022-11-29 [1] RSPM (R > 4.5.0) > purrr 1.1.0 2025-07-10 [1] RSPM (R > 4.5.0) > R6 2.6.1 2025-02-15 [1] RSPM (R > 4.5.0) > rappdirs 0.3.3 2021-01-31 [1] RSPM (R > 4.5.0) > RColorBrewer 1.1-3 2022-04-03 [1] RSPM (R > 4.5.0) > Rcpp 1.1.0 2025-07-02 [1] RSPM (R > 4.5.0) > RCurl 1.98-1.17 2025-03-22 [1] RSPM (R > 4.5.0) > readr 2.1.5 2024-01-10 [1] RSPM (R > 4.5.0) > regioneR 1.41.3 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > remotes 2.5.0 2024-03-17 [1] RSPM (R > 4.5.0) > reshape2 1.4.4 2020-04-09 [1] RSPM (R > 4.5.0) > restfulr 0.0.16 2025-06-27 [1] RSPM (R > 4.5.1) > rjson 0.2.23 2024-09-16 [1] RSPM (R > 4.5.0) > rlang 1.1.6 2025-04-11 [1] RSPM (R > 4.5.0) > rprojroot 2.1.1 2025-08-26 [1] RSPM (R > 4.5.0) > Rsamtools 2.25.3 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > RSQLite 2.4.3 2025-08-20 [1] RSPM (R > 4.5.0) > rstudioapi 0.17.1 2024-10-22 [1] RSPM (R > 4.5.0) > rtracklayer * 1.69.1 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > S4Arrays 1.9.1 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > S4Vectors * 0.47.4 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > S7 0.2.0 2024-11-07 [1] RSPM (R > 4.5.0) > scales 1.4.0 2025-04-24 [1] RSPM (R > 4.5.0) > Seqinfo * 0.99.2 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > sessioninfo 1.2.3 2025-02-05 [1] RSPM (R > 4.5.0) > SparseArray 1.9.1 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > stringi 1.8.7 2025-03-27 [1] RSPM (R > 4.5.0) > stringr 1.5.2 2025-09-08 [1] RSPM (R > 4.5.0) > SummarizedExperiment 1.39.2 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > testthat * 3.2.3 2025-01-13 [1] RSPM (R > 4.5.0) > tibble 3.3.0 2025-06-08 [1] RSPM (R > 4.5.0) > tidyselect 1.2.1 2024-03-11 [1] RSPM (R > 4.5.0) > TxDb.Hsapiens.UCSC.hg19.knownGene * 3.22.0 2025-10-11 [1] > Bioconductor > tzdb 0.5.0 2025-03-15 [1] RSPM (R > 4.5.0) > UCSC.utils 1.5.0 2025-04-17 [1] > Bioconductor 3.22 (R 4.5.0) > usethis 3.2.1 2025-09-06 [1] RSPM (R > 4.5.0) > vctrs 0.6.5 2023-12-01 [1] RSPM (R > 4.5.0) > withr 3.0.2 2024-10-28 [1] RSPM (R > 4.5.0) > XML 3.99-0.19 2025-08-22 [1] RSPM (R > 4.5.0) > XVector 0.49.1 2025-10-07 [1] > Bioconductor 3.22 (R 4.5.1) > yaml 2.3.10 2024-07-26 [1] RSPM (R > 4.5.0) > > Thanks! > > -------------------- > Raymond Cavalcante, PhD > Bioinformatics Analyst > Epigenomics Core and Bioinformatics Core > Biomedical Research Core Facilities > University of Michigan Medical School > > [email protected] > [email protected] > > 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