I am aligning some PacBio single read sequences using Blasr. I was able to successfully align and create a Sam file for some of my sequences, but some report a sam file that begins like the following:
@HD VN:1.5 SO:UNKNOWN pb:3.0.1
@SQ SN:gi/0/0_1667892 LN:1667892 M5:f8a1580a28e068939d886d1c70879a72
@RG ID:95680781 PL:PACBIO DS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq PU:/home/akm126/HpGP_Data/HON001_edit.fasta PM:SEQUEL
@PG ID:1 PN:BLASR VN:5.3.3 CL:blasr /home/akm126/HpGP_Data/HON001_edit.fasta /home/akm126/HpGP_Data/HP_bacteria/HP_bacteria.fasta --sam --out alignment1_test.sam
Rabkin_HON001/0/0_166079401 16 gi/0/0_1667892 1751 254 47825S25=1D1=2D1=1D2=3D1=1D1=1D45=2D1=5D1=1D8=1X1=1X39=2D1=3D1=2D46=1X4=6D10=1X44=1D2=2
D1=1D2=1D4=1X29=1X2=1X2=1D1=1I2=1X2=2D2=1D1=1D41=1X1=1X11=3D39=1X11=1X6=2D2=1X55=1D18=1X6=1X43=1I1=1D9=1X1=1X13=1X21=1X24=1X18=2X13=1D21=1X1=1X24= 1X8=1X2D55=2D1=1D54=1I2=3D1=2D5=1X1D5=1X2=1X4=1D1=2I26=1X1=1X1=2D1=1D1=2D49=1X1D2
I can't find any differences in the header between files. Any ideas why the "1D1=1D2" is happening? Thanks.
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