I am doing alignment using BWA mem using command
bwa index -p H37Rv_reference_genome -a bwtsw GCF_000195955.2_ASM19595v2_genomic.fasta bwa mem H37Rv_reference_genome ERR3566420_1.fastq ERR3566420_2_trimmed.fastq >ERR3566420.sam samtools view -bS ERR3566420.sam >ERR3566420.bam samtools flagstat ERR3566420.bam
Now when I am seeing the percentage of the mapped reads I am seeing really less alignment to be precise (8.83%) paired and (7.19%) properly paired. My question is if both are related species of Mycobacterium how they are having such low alignment. Do I need to make come changes in the parameters?
Also I used Kraken tool for the alignment using this command
./kraken2 --db mycobacterium_database/ --threads 20 SRR8594817_1.fastq SRR8594817_2.fastq >SRR8594817_kraken.txt
So the results from this is (99.07%) alignment.
I am not able to understand that why am I getting such low alignment using BWA tool having reference genome as H37Rv genome and why the results from the Kraken tool are so contradictory.
Kindly help me with the possible suggestion, Thanks.