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:	3585012
Total number duplicated alignments removed:	150670 (4.20%)
Duplicated alignments were found at:	126749 different position(s)

Total count of deduplicated leftover sequences: 3434342 (95.80% 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:	2299993
Total number duplicated alignments removed:	73049 (3.18%)
Duplicated alignments were found at:	58714 different position(s)

Total count of deduplicated leftover sequences: 2226944 (96.82% 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:	5898473
Total number duplicated alignments removed:	357487 (6.06%)
Duplicated alignments were found at:	289095 different position(s)

Total count of deduplicated leftover sequences: 5540986 (93.94% 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:	6143399
Total number duplicated alignments removed:	356192 (5.80%)
Duplicated alignments were found at:	275036 different position(s)

Total count of deduplicated leftover sequences: 5787207 (94.20% 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:	5194561
Total number duplicated alignments removed:	168028 (3.23%)
Duplicated alignments were found at:	142341 different position(s)

Total count of deduplicated leftover sequences: 5026533 (96.77% 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:	6213355
Total number duplicated alignments removed:	373151 (6.01%)
Duplicated alignments were found at:	312001 different position(s)

Total count of deduplicated leftover sequences: 5840204 (93.99% 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:	5127457
Total number duplicated alignments removed:	186706 (3.64%)
Duplicated alignments were found at:	155273 different position(s)

Total count of deduplicated leftover sequences: 4940751 (96.36% 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:	5560803
Total number duplicated alignments removed:	222796 (4.01%)
Duplicated alignments were found at:	193251 different position(s)

Total count of deduplicated leftover sequences: 5338007 (95.99% 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:	5162019
Total number duplicated alignments removed:	253566 (4.91%)
Duplicated alignments were found at:	215890 different position(s)

Total count of deduplicated leftover sequences: 4908453 (95.09% 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:	6030681
Total number duplicated alignments removed:	823325 (13.65%)
Duplicated alignments were found at:	669678 different position(s)

Total count of deduplicated leftover sequences: 5207356 (86.35% of total)