Hello, I have a bam file and the output of flagstat is

**2081062 + 0 in total (QC-passed reads + QC-failed reads)**
**1434239 + 0 secondary**
13883 + 0 supplementary
0 + 0 duplicates
2057380 + 0 mapped (98.86% : 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)

stats:

**raw total sequences:  632940**
filtered sequences: 0
sequences:  632940
is sorted:  0
1st fragments:  632940
last fragments: 0
reads mapped:   609258
reads mapped and paired:    0   # paired-end technology bit set + both mates mapped
reads unmapped: 23682
reads properly paired:  0   # proper-pair bit set
reads paired:   0   # paired-end technology bit set
reads duplicated:   0   # PCR or optical duplicate bit set
reads MQ0:  246308  # mapped and MQ=0
reads QC failed:    0
**non-primary alignments:   1434239**
total length:   580845355   # ignores clipping
total first fragment length:    580845355   # ignores clipping
total last fragment length: 0   # ignores clipping
bases mapped:   569218429   # ignores clipping
bases mapped (cigar):   536472283   # more accurate
bases trimmed:  0
bases duplicated:   0
mismatches: 71417634    # from NM fields
error rate: 1.331245e-01    # mismatches / bases mapped (cigar)
average length: 917
average first fragment length:  918
average last fragment length:   0
maximum length: 18968
maximum first fragment length:  0
maximum last fragment length:   0
average quality:    16.3
insert size average:    0.0
insert size standard deviation: 0.0
inward oriented pairs:  0
outward oriented pairs: 0
pairs with other orientation:   0
pairs on different chromosomes: 0
percentage of properly paired reads (%):    0.0

Really I have 632940 reads. I don't understand the number of 2 millions in flagstat, how could it be so? I'd like to find the reads with secondary alignment. Firstly, I'd like to know how many reads I have with secondary alignment.

Thank you a lot.

P.s I've read about 2081062 - 1434239 - 13883 = 632940. But it didn't help me with understanding the number 2081062. Also idxstats sorted.bam | awk '{s+=$3+$4} END {print s}' gives me 2081062. Alignment with human transcriptome.