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 Mapped29526898.696%
Wrongly Mapped38821.298%
Not Mapped180.006%
Total299168100.0%
Read Failure Statistics
Not mapped180.006%
Missing in mapper output00.0%
Mapped to wrong chromosome9840.329%
Mapped to wrong position28980.969%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.993400
Precision0.987000
Recall0.999900
Timing
Raw Mapping Time89.652s
Effective Mapping Time89.116s
Effective Init Time0.536s
Effective Time MeasureCPU
Mapping Time (Wall)25.946s
Mapping Time (CPU)89.652s
Mapping Time (CPU User)85.928s
Mapping Time (CPU System)3.724s
Init Time (Wall)0.490s
Init Time (CPU)0.536s
Init Time (CPU User)0.148s
Init Time (CPU System)0.388s
Additional Information
Mapper Memory Usage221 MB
Total Test Runtime (Wall)99.439s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory196520000
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
systime0.432
time13.7796390057
usrtime0.148
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory194476000
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
systime0.388
time0.489768028259
usrtime0.148
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory221632000
return0
status1
stderr
None
stdout
149584 reads; of these:
149584 (100.00%) were paired; of these:
159 (0.11%) aligned concordantly 0 times
132710 (88.72%) aligned concordantly exactly 1 time
16715 (11.17%) aligned concordantly >1 times
----
159 pairs aligned concordantly 0 times; of these:
119 (74.84%) aligned discordantly 1 time
----
40 pairs aligned 0 times concordantly or discordantly; of these:
80 mates make up the pairs; of these:
18 (22.50%) aligned 0 times
19 (23.75%) aligned exactly 1 time
43 (53.75%) aligned >1 times
99.99% overall alignment rate
systime3.724
time25.9459950924
usrtime85.928
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300