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 Mapped48510997.291%
Wrongly Mapped131492.637%
Not Mapped3560.071%
Total498614100.0%
Read Failure Statistics
Not mapped3560.071%
Missing in mapper output00.0%
Mapped to wrong chromosome51251.028%
Mapped to wrong position80241.609%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.986300
Precision0.973600
Recall0.999300
Timing
Raw Mapping Time92.876s
Effective Mapping Time92.348s
Effective Init Time0.528s
Effective Time MeasureCPU
Mapping Time (Wall)28.897s
Mapping Time (CPU)92.876s
Mapping Time (CPU User)90.472s
Mapping Time (CPU System)2.404s
Init Time (Wall)0.484s
Init Time (CPU)0.528s
Init Time (CPU User)0.136s
Init Time (CPU System)0.392s
Additional Information
Mapper Memory Usage217 MB
Total Test Runtime (Wall)130.319s
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
memory196524000
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
systime0.46
time13.9114279747
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

/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
systime0.392
time0.484041929245
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

/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
memory217236000
return0
status1
stderr
None
stdout
249307 reads; of these:
249307 (100.00%) were paired; of these:
27938 (11.21%) aligned concordantly 0 times
189633 (76.06%) aligned concordantly exactly 1 time
31736 (12.73%) aligned concordantly >1 times
----
27938 pairs aligned concordantly 0 times; of these:
23251 (83.22%) aligned discordantly 1 time
----
4687 pairs aligned 0 times concordantly or discordantly; of these:
9374 mates make up the pairs; of these:
356 (3.80%) aligned 0 times
502 (5.36%) aligned exactly 1 time
8516 (90.85%) aligned >1 times
99.93% overall alignment rate
systime2.404
time28.897231102
usrtime90.472
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af