Processing paired-end Bismark output file(s) (SAM format):
zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam:	5299
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 5299 (100.00% of total)

Checking file >>zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam:	2878
Total number duplicated alignments removed:	6 (0.21%)
Duplicated alignments were found at:	6 different position(s)

Total count of deduplicated leftover sequences: 2872 (99.79% of total)

Checking file >>zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam:	4978
Total number duplicated alignments removed:	2 (0.04%)
Duplicated alignments were found at:	2 different position(s)

Total count of deduplicated leftover sequences: 4976 (99.96% of total)

Checking file >>zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam:	5359
Total number duplicated alignments removed:	1 (0.02%)
Duplicated alignments were found at:	1 different position(s)

Total count of deduplicated leftover sequences: 5358 (99.98% of total)

Checking file >>zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam:	5293
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 5293 (100.00% of total)

Checking file >>zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam:	5173
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 5173 (100.00% of total)

Checking file >>zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam:	5375
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 5375 (100.00% of total)

Checking file >>zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam:	5144
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 5144 (100.00% of total)

Checking file >>zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam:	4760
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 4760 (100.00% of total)

Checking file >>zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...
...passed!
Output file is: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam

[samopen] SAM header is present: 11 sequences.

Total number of alignments analysed in zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam:	4994
Total number duplicated alignments removed:	0 (0.00%)
Duplicated alignments were found at:	0 different position(s)

Total count of deduplicated leftover sequences: 4994 (100.00% of total)