[Bioc-devel] hg19 has two mitochondrial chromosomes in Seqinfo
Tim Triche, Jr.
t|m@tr|che @end|ng |rom gm@||@com
Sun Oct 12 18:57:28 CEST 2025
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 <rcavalca using umich.edu> 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
>
> rcavalca using umich.edu
> rcavalca using med.umich.edu
>
> [[alternative HTML version deleted]]
>
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