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 Mapped52754288.091%
Wrongly Mapped6942311.593%
Not Mapped18930.316%
Total598858100.0%
Read Failure Statistics
Not mapped18930.316%
Missing in mapper output00.0%
Mapped to wrong chromosome414066.914%
Mapped to wrong position280174.678%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936700
Precision0.883700
Recall0.996400
Timing
Raw Mapping Time71.612s
Effective Mapping Time69.036s
Effective Init Time2.576s
Effective Time MeasureCPU
Mapping Time (Wall)32.033s
Mapping Time (CPU)71.612s
Mapping Time (CPU User)66.096s
Mapping Time (CPU System)5.516s
Init Time (Wall)2.643s
Init Time (CPU)2.576s
Init Time (CPU User)0.160s
Init Time (CPU System)2.416s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)166.280s
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
memory222044000
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
systime2.78
time16.2699949741
usrtime0.172
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0

/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
memory220972000
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
systime2.416
time2.64291000366
usrtime0.16
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0

/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
memory236284000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1893 (0.32%) aligned 0 times
484243 (80.86%) aligned exactly 1 time
112722 (18.82%) aligned >1 times
99.68% overall alignment rate
systime5.516
time32.0327830315
usrtime66.096
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0