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 Mapped76449185.105%
Wrongly Mapped11461012.759%
Not Mapped191862.136%
Total898287100.0%
Read Failure Statistics
Not mapped191862.136%
Missing in mapper output00.0%
Mapped to wrong chromosome723038.049%
Mapped to wrong position423074.71%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.919500
Precision0.869600
Recall0.975500
Timing
Raw Mapping Time66.492s
Effective Mapping Time65.880s
Effective Init Time0.612s
Effective Time MeasureCPU
Mapping Time (Wall)29.565s
Mapping Time (CPU)66.492s
Mapping Time (CPU User)64.752s
Mapping Time (CPU System)1.740s
Init Time (Wall)0.559s
Init Time (CPU)0.612s
Init Time (CPU User)0.120s
Init Time (CPU System)0.492s
Additional Information
Mapper Memory Usage322 MB
Total Test Runtime (Wall)114.007s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory322468000
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
systime0.556
time15.8831479549
usrtime0.16
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory322468000
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
systime0.492
time0.558670043945
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory322468000
return0
status1
stderr
None
stdout
898287 reads; of these:
898287 (100.00%) were unpaired; of these:
19186 (2.14%) aligned 0 times
714056 (79.49%) aligned exactly 1 time
165045 (18.37%) aligned >1 times
97.86% overall alignment rate
systime1.74
time29.5648319721
usrtime64.752
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef