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 Mapped52660487.935%
Wrongly Mapped7037011.751%
Not Mapped18840.315%
Total598858100.0%
Read Failure Statistics
Not mapped18840.315%
Missing in mapper output00.0%
Mapped to wrong chromosome425067.098%
Mapped to wrong position278644.653%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.935800
Precision0.882100
Recall0.996400
Timing
Raw Mapping Time80.488s
Effective Mapping Time79.852s
Effective Init Time0.636s
Effective Time MeasureCPU
Mapping Time (Wall)32.070s
Mapping Time (CPU)80.488s
Mapping Time (CPU User)78.428s
Mapping Time (CPU System)2.060s
Init Time (Wall)0.631s
Init Time (CPU)0.636s
Init Time (CPU User)0.152s
Init Time (CPU System)0.484s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)123.300s
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
memory221816000
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
systime0.52
time15.9779031277
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8

/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
memory228736000
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
systime0.484
time0.630872011185
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8

/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
memory236300000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1884 (0.31%) aligned 0 times
483528 (80.74%) aligned exactly 1 time
113446 (18.94%) aligned >1 times
99.69% overall alignment rate
systime2.06
time32.0700371265
usrtime78.428
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8