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 Mapped30277396.512%
Wrongly Mapped107533.428%
Not Mapped1900.061%
Total313716100.0%
Read Failure Statistics
Not mapped1900.061%
Missing in mapper output00.0%
Mapped to wrong chromosome69272.208%
Mapped to wrong position38261.22%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.982200
Precision0.965700
Recall0.999400
Timing
Raw Mapping Time151.372s
Effective Mapping Time147.908s
Effective Init Time3.464s
Effective Time MeasureCPU
Mapping Time (Wall)46.877s
Mapping Time (CPU)151.372s
Mapping Time (CPU User)142.800s
Mapping Time (CPU System)8.572s
Init Time (Wall)3.418s
Init Time (CPU)3.464s
Init Time (CPU User)0.140s
Init Time (CPU System)3.324s
Additional Information
Mapper Memory Usage3410 MB
Total Test Runtime (Wall)119.427s
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
memory3359448000
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
systime3.168
time3.23244190216
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38

/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
memory3359364000
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
systime3.324
time3.41814303398
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38

/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
memory3410888000
return0
status1
stderr
None
stdout
156858 reads; of these:
156858 (100.00%) were paired; of these:
77175 (49.20%) aligned concordantly 0 times
68290 (43.54%) aligned concordantly exactly 1 time
11393 (7.26%) aligned concordantly >1 times
----
77175 pairs aligned concordantly 0 times; of these:
63891 (82.79%) aligned discordantly 1 time
----
13284 pairs aligned 0 times concordantly or discordantly; of these:
26568 mates make up the pairs; of these:
190 (0.72%) aligned 0 times
2472 (9.30%) aligned exactly 1 time
23906 (89.98%) aligned >1 times
99.94% overall alignment rate
systime8.572
time46.8766260147
usrtime142.8
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38