Number of pairs analyzed ...............................	2500
Prefix failed in read 1 ................................	0
Prefix failed in read 2 ................................	0
Prefix failed in both ..................................	0
Passed prefix total ....................................	2500
Failed prefix total ....................................	0
Merged total ...........................................	1660
Complete overlap forced total ..........................	203
Merge failed total .....................................	840
Merge discarded due to P ...............................	443
Merge discarded due to max num mismatches ..............	0
Merge discarded due to Ns ..............................	58
Merge discarded due to Q30 .............................	339
Pairs discarded due to min expected overlap ............	0
Num mismatches found in merged reads ...................	339
Mismatches recovered from read 1 .......................	269
Mismatches recovered from read 2 .......................	70
Mismatches replaced with N .............................	0


Mismatches breakdown in final merged reads:

0	1455
1	144
2	33
3	10
4	5
5	5
6	5
7	1
8	1
9	1


Command line ...........................................	/Users/meren/github/illumina-utils/scripts/iu-merge-pairs hiseq_partial_overlap_config.ini --enforce-Q30-check --marker-gene-str
Work directory .........................................	/Users/meren/github/illumina-utils/examples/merging
"p" value ..............................................	0.300000
Max num mismatches at the overlapped region ............	None
Min overlap size .......................................	15
Min Q-score for mismatches .............................	15
Ns ignored? ............................................	False
Q30 enforced? ..........................................	True
Run with stringent flag on? ............................	True
Requested only the overlapping part to be retained? ....	False
