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 Mapped29263397.544%
Wrongly Mapped49471.649%
Not Mapped24200.807%
Total300000100.0%
Read Failure Statistics
Not mapped24200.807%
Missing in mapper output00.0%
Mapped to wrong chromosome40081.336%
Mapped to wrong position9390.313%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.987600
Precision0.983400
Recall0.991800
Timing
Raw Mapping Time20.612s
Effective Mapping Time20.220s
Effective Init Time0.392s
Effective Time MeasureCPU
Mapping Time (Wall)10.629s
Mapping Time (CPU)20.612s
Mapping Time (CPU User)19.632s
Mapping Time (CPU System)0.980s
Init Time (Wall)0.351s
Init Time (CPU)0.392s
Init Time (CPU User)0.132s
Init Time (CPU System)0.260s
Additional Information
Mapper Memory Usage81 MB
Total Test Runtime (Wall)63.753s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads.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/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory72104000
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
systime0.264
time2.66283297539
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory74148000
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
systime0.26
time0.351171970367
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory81148000
return0
status1
stderr
None
stdout
300000 reads; of these:
300000 (100.00%) were unpaired; of these:
2420 (0.81%) aligned 0 times
285798 (95.27%) aligned exactly 1 time
11782 (3.93%) aligned >1 times
99.19% overall alignment rate
systime0.98
time10.6288869381
usrtime19.632
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a