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 Mapped52778788.132%
Wrongly Mapped6917011.55%
Not Mapped19010.317%
Total598858100.0%
Read Failure Statistics
Not mapped19010.317%
Missing in mapper output00.0%
Mapped to wrong chromosome410216.85%
Mapped to wrong position281494.7%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936900
Precision0.884100
Recall0.996400
Timing
Raw Mapping Time139.156s
Effective Mapping Time129.852s
Effective Init Time9.304s
Effective Time MeasureCPU
Mapping Time (Wall)52.726s
Mapping Time (CPU)139.156s
Mapping Time (CPU User)126.640s
Mapping Time (CPU System)12.516s
Init Time (Wall)9.539s
Init Time (CPU)9.304s
Init Time (CPU User)0.156s
Init Time (CPU System)9.148s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)207.816s
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
memory222040000
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
systime6.512
time16.1583900452
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

/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
memory218496000
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
systime9.148
time9.5391728878
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

/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
memory236468000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1901 (0.32%) aligned 0 times
484994 (80.99%) aligned exactly 1 time
111963 (18.70%) aligned >1 times
99.68% overall alignment rate
systime12.516
time52.7261059284
usrtime126.64
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b