I think I figured it out -

It looks like 60970 reads in flagstat includes the supplementary reads while stats does not count it. 52505 + 8465 = 60970

I have an example where raw total sequences: from the samstats is the same as QC-passed reads(flagstat) - secondary (flagstat), so note that it could be that raw total sequences(samstat) = QC-passed reads(flagstat) - secondary (flagstat) - supplementary (flagstat)

but I'm not sure. This is my example:

flagstat:

16233358 + 0 in total (QC-passed reads + QC-failed reads) 2194850 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 15871381 + 0 mapped (97.77% : 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)

samts:

This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats

This file contains statistics for all reads.

The command line was: stats rep1_local_aligned.sam

CHK, Checksum [2]Read Names [3]Sequences [4]Qualities

CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)

CHK 2c2dd00f 8a348144 a42ae467

Summary Numbers. Use grep ^SN | cut -f 2- to extract this part.

SN raw total sequences: 14038508 SN filtered sequences: 0 SN sequences: 14038508 SN is sorted: 0 SN 1st fragments: 14038508 SN last fragments: 0 SN reads mapped: 13676531 SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped SN reads unmapped: 361977 SN reads properly paired: 0 # proper-pair bit set SN reads paired: 0 # paired-end technology bit set SN reads duplicated: 0 # PCR or optical duplicate bit set SN reads MQ0: 394 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 2194850 SN total length: 1027717498 # ignores clipping SN total first fragment length: 1027717498 # ignores clipping SN total last fragment length: 0 # ignores clipping SN bases mapped: 1001586559 # ignores clipping SN bases mapped (cigar): 998852161 # more accurate SN bases trimmed: 0 SN bases duplicated: 0 SN mismatches: 2103263 # from NM fields SN error rate: 2.105680e-03 # mismatches / bases mapped (cigar) SN average length: 73 SN average first fragment length: 73 SN average last fragment length: 0 SN maximum length: 75 SN maximum first fragment length: 0 SN maximum last fragment length: 0 SN average quality: 34.2 SN insert size average: 0.0 SN insert size standard deviation: 0.0 SN inward oriented pairs: 0 SN outward oriented pairs: 0 SN pairs with other orientation: 0 SN pairs on different chromosomes: 0 SN percentage of properly paired reads (%): 0.0