Hi all!

I was trying to map sequences to genome contigs. To do that I've performed commands:

bwa index ref.fasta
bwa mem ref.fasta input.fasta > aln.sam
samtools view -Sb aln.sam > aln.bam
samtools sort aln.bam > aln_sorted.bam
samtools flagstat aln_sorted.bam > aln_stats.txt

input. fasta include 3158 sequences.

Here is aln_stats.txt output:

 5284 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 secondary
    2126 + 0 supplementary
    0 + 0 duplicates
    4890 + 0 mapped (92.54% : N/A)
    0 + 0 paired in sequencing
    0 + 0 read1
    0 + 0 read2
    0 + 0 properly paired (N/A : N/A)
    0 + 0 with itself and mate mapped
    0 + 0 singletons (N/A : N/A)
    0 + 0 with mate mapped to a different chr
    0 + 0 with mate mapped to a different chr (mapQ>=5)

Why output includs 5284 sequences in total?

I see that 2126 is supplementary, 5284 - 2126 = 3158, which is the number of sequences in input.

Thanks in advance, Best, Agata