Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped20477597.911%
Wrongly Mapped43192.065%
Not Mapped500.024%
Total209144100.0%
Read Failure Statistics
Not mapped500.024%
Missing in mapper output00.0%
Mapped to wrong chromosome27621.321%
Mapped to wrong position15570.744%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.989400
Precision0.979300
Recall0.999800
Timing
Raw Mapping Time151.040s
Effective Mapping Time147.532s
Effective Init Time3.508s
Effective Time MeasureCPU
Mapping Time (Wall)44.470s
Mapping Time (CPU)151.040s
Mapping Time (CPU User)145.460s
Mapping Time (CPU System)5.580s
Init Time (Wall)3.496s
Init Time (CPU)3.508s
Init Time (CPU User)0.120s
Init Time (CPU System)3.388s
Additional Information
Mapper Memory Usage3414 MB
Total Test Runtime (Wall)87.353s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359292000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime3.392
time3.55389595032
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3361392000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime3.388
time3.49622392654
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory3414296000
return0
status1
stderr
None
stdout
104572 reads; of these:
104572 (100.00%) were paired; of these:
161 (0.15%) aligned concordantly 0 times
92994 (88.93%) aligned concordantly exactly 1 time
11417 (10.92%) aligned concordantly >1 times
----
161 pairs aligned concordantly 0 times; of these:
106 (65.84%) aligned discordantly 1 time
----
55 pairs aligned 0 times concordantly or discordantly; of these:
110 mates make up the pairs; of these:
50 (45.45%) aligned 0 times
8 (7.27%) aligned exactly 1 time
52 (47.27%) aligned >1 times
99.98% overall alignment rate
systime5.58
time44.4699621201
usrtime145.46
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12