missing chromosome in annotation for RNAseq data

[Wannes Dermauw]

Hi

I have the following output for RNAseq PE data:

Analysis date:  Thu May 11 09:34:46 CEST 2023

BAM file:   Sample_41807791_Q20.bam

Counting algorithm: uniquely-mapped-reads

GTF file:   ASM185493v1_genomic.gtf

Paired-end sequencing:  no

Protocol:   non-strand-specific

Sorting performed:  no

Summary

Reads alignment

Number of mapped reads: 19,536,818

Total number of alignments: 19,536,818

Number of secondary alignments: 0

Number of non-unique alignments:    0

Aligned to genes:   1,664,906

Ambiguous alignments:   419

No feature assigned:    5,495,465

Missing chromosome in annotation:   12,376,028

Not aligned:    0

Strand specificity estimation (fwd/rev):    0.46 / 0.54

and noticed a > 50 % of aligned reads with "missing chromosome in annotation".

Based on other Qualimap outputs (based on a google search) this seems very high, and I wondered what the cause might be of such high %.

Any help would be much appreciated.

Kind regards

Wannes

PS: the gtf used for RNA read mapping in STAR was GCF_001854935.1_ASM185493v1_genomic.gtf.gz available at https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/854/935/GCF_001854935.1_ASM185493v1/