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 Mapped52754888.092%
Wrongly Mapped6941111.591%
Not Mapped18990.317%
Total598858100.0%
Read Failure Statistics
Not mapped18990.317%
Missing in mapper output00.0%
Mapped to wrong chromosome413076.898%
Mapped to wrong position281044.693%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936700
Precision0.883700
Recall0.996400
Timing
Raw Mapping Time65.028s
Effective Mapping Time64.440s
Effective Init Time0.588s
Effective Time MeasureCPU
Mapping Time (Wall)28.293s
Mapping Time (CPU)65.028s
Mapping Time (CPU User)62.904s
Mapping Time (CPU System)2.124s
Init Time (Wall)0.573s
Init Time (CPU)0.588s
Init Time (CPU User)0.140s
Init Time (CPU System)0.448s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)148.926s
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
memory224164000
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
time16.3304610252
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0

/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
memory222204000
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
systime0.448
time0.573447942734
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0

/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
memory236548000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1899 (0.32%) aligned 0 times
484833 (80.96%) aligned exactly 1 time
112126 (18.72%) aligned >1 times
99.68% overall alignment rate
systime2.124
time28.2929918766
usrtime62.904
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0