This file is indexed.

/usr/lib/R/site-library/Rsamtools/INDEX is in r-bioc-rsamtools 1.16.1-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

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BamFile                 Maintain and use BAM files
BamSampler              Sample from a BAM files
BamViews                Views into a set of BAM files
BcfFile                 Manipulate BCF files.
FaFile                  Manipulate indexed fasta files.
PileupFiles             Represent BAM files for pileup summaries.
PileupParam             Parameters for creating pileups from BAM files
Rsamtools-package       'samtools' aligned sequence utilities interface
RsamtoolsFile-class     A base class for managing file references in
                        Rsamtools
RsamtoolsFileList       A base class for managing lists of Rsamtools
                        file references
ScanBamParam            Parameters for scanning BAM files
ScanBcfParam-class      Parameters for scanning BCF files
TabixFile               Manipulate tabix indexed tab-delimited files.
applyPileups            Create summary pile-up statistics across
                        multiple BAM files.
bgzip                   File compression for tabix (bgzip) and fasta
                        (razip) files.
headerTabix             Retrieve sequence names defined in a tabix
                        file.
indexFa                 Operations on indexed 'fasta' files.
indexTabix              Compress and index tabix-compatible files.
quickBamFlagSummary     Group the records of a BAM file based on their
                        flag bits and count the number of records in
                        each group
readPileup              Import samtools 'pileup' files.
scanBam                 Import, count, index, filter, sort, and merge
                        'BAM' (binary alignment) files.
scanBcfHeader           Operations on 'BCF' files.
scanTabix               Operations on 'tabix' (indexed, tab-delimited)
                        files.
seqnamesTabix           Retrieve sequence names defined in a tabix
                        file.
yieldReduce             Iterate through a BAM (or other) file, reducing
                        output to a single result.
yieldTabix              Deprecated functions