Check the GTF/GFF annotation file used in the featureCounts step, which may contain multiple entries for the same gene due to alternative splice variants or different isoforms. Some genes in the human genome may have duplicate entries due to pseudogenes or closely related gene families, leading to ambiguity during gene counting. Ensure the genome annotation file is compatible with the version of the genome aligned with your reads to avoid discrepancies. Review the naming conventions used in the annotation file, as some databases or annotation sources may append "_1" or other suffixes to gene names. To address this situation, carefully review the annotation file, verify if "ABO" and "ABO_1" represent the same gene, filter out one of the duplicates. Double-checking the annotation file and understanding the source of these duplicate entries is crucial for a valid RNA-seq analysis.

Susanta Roy Thank you for the clarification, My genome file and annotation file are compatible, both are from p14 version, i didn't encounter such problem with p13, version. As p14 is most recent so took that. Though i will check that GTF file to detect the source of such problem.

I think the gene ID in your GTF or GFF3 files you used for constructing the alignment index might not be the transcript ID including splice variant, which cause multiple alignment to 1 gene. I think you'd better use the genome annotation file and sequence file (gtf and fa) file from the ensembl (with gtf available at https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz and fa at https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) or download pre-bulit index from the website or your alignment tools.