I saw lot of record with perfect alignment (150M) but marked as secondary alignment in SAM file. For example those with FLAG number 339 or 419. The following one for example:
E00477:134:H2H2NCCXx:6:2203:29267:71384 419 chr1 14479 3 150M = 14705 376 GTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGCTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTC AAAFFK<AF<A<AFFFKFKFKKKKKKKK7FK<AKAA7AFKFKK<FFKKKKKKKAKKKKKKKF,,7AAFKAK,,<AFFKKK7,,<FKKKKFAK7AFF<,AFA7AAA<K(FKKKA,,<FFAK7AK(,AFAF7,,7AFF,,<AA77,<77FAA NH:i:2 HI:i:2 AS:i:296 nM:i:1
Why is that? Does that mean their corresponding primary alignment is also perfect and has higher base call quality? Any comments are appreciated!