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Sequence Coordinates

Source: vignettes/articles/sequence_coordinates.Rmd
sequence_coordinates.Rmd

The MGI report MGI_GTGUP.gff1 is a comprehensive list of mouse genetic markers (> 2,900,000) spanning various marker types:

  • Genes: ~ 55,000 markers
  • Gene Models: ~ 2,300,000 markers
  • Pseudogenes: ~ 15,000 markers
  • Transgenes: ~ 30 markers
  • Cytogenetic Markers: ~ 130 markers
  • Complex/Cluster/Region: ~ 60 markers
  • Other Genome Feature: ~ 560,000 markers

To read this report using the key "sequence_coordinates", use the following code:

# To read all records (more than 2,900,000), use `read_report("sequence_coordinates")`.
(sequence_coord <- read_report(report_key = "sequence_coordinates", n_max = 300L))
## # A tibble: 300 × 9
##    marker_type    marker_id marker_symbol chromosome  start    end strand source
##    <fct>          <chr>     <chr>         <fct>       <int>  <int> <fct>  <fct> 
##  1 Other Genome … MGI:6903… Rr15647       1          3.05e6 3.05e6 NA     MGI   
##  2 Other Genome … MGI:6914… Rr26566       1          3.05e6 3.05e6 NA     MGI   
##  3 Other Genome … MGI:6914… Rr26567       1          3.05e6 3.05e6 NA     MGI   
##  4 Other Genome … MGI:6903… Rr15649       1          3.06e6 3.06e6 NA     MGI   
##  5 Other Genome … MGI:6914… Rr26568       1          3.06e6 3.06e6 NA     MGI   
##  6 Other Genome … MGI:6914… Rr26571       1          3.06e6 3.06e6 NA     MGI   
##  7 Other Genome … MGI:6903… Rr15664       1          3.08e6 3.08e6 NA     MGI   
##  8 Other Genome … MGI:6914… Rr26579       1          3.10e6 3.10e6 NA     MGI   
##  9 Other Genome … MGI:6924… Rr36329       1          3.12e6 3.12e6 NA     MGI   
## 10 Other Genome … MGI:6924… Rr36333       1          3.13e6 3.13e6 NA     MGI   
## # ℹ 290 more rows
## # ℹ 1 more variable: feature_type <fct>

Variables

marker_type

marker_type: genetic marker type is a factor of 10 levels: Gene, GeneModel, Pseudogene, DNA Segment, Transgene, QTL, Cytogenetic Marker, BAC/YAC end, Complex/Cluster/Region, Other Genome Feature. See ?marker_type_definitions for the meaning of each type.

marker_id

marker_id: MGI accession identifier. A unique alphanumeric character string that is used to unambiguously identify a particular record in the Mouse Genome Informatics database. The format is MGI:nnnnnn, where n is a digit.

marker_symbol

marker_symbol: marker symbol is a unique abbreviation of the marker name.

marker_name

marker_name: marker name is a word or phrase that uniquely identifies the genetic marker, e.g. a gene or allele name.

chromosome

chromosome: mouse chromosome name. Possible values are names for the autosomal, sexual or mitochondrial chromosomes.

start

start: genomic start position (one-offset).

end

end: genomic end position (one-offset).

strand

strand: DNA strand, ‘+’ for sense, and ‘-’ for antisense.

source

source: provider of the genomic annotation.

feature_type

feature_type: an attribute of a portion of a genomic sequence. See the dataset ?feature_type_definitions for details.