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 Mapped32366290.078%
Wrongly Mapped356069.909%
Not Mapped460.013%
Total359314100.0%
Read Failure Statistics
Not mapped460.013%
Missing in mapper output00.0%
Mapped to wrong chromosome200095.569%
Mapped to wrong position155974.341%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.947800
Precision0.900900
Recall0.999900
Timing
Raw Mapping Time60.440s
Effective Mapping Time59.828s
Effective Init Time0.612s
Effective Time MeasureCPU
Mapping Time (Wall)27.030s
Mapping Time (CPU)60.440s
Mapping Time (CPU User)58.864s
Mapping Time (CPU System)1.576s
Init Time (Wall)0.579s
Init Time (CPU)0.612s
Init Time (CPU User)0.156s
Init Time (CPU System)0.456s
Additional Information
Mapper Memory Usage239 MB
Total Test Runtime (Wall)99.213s
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
memory222048000
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
systime0.66
time17.896985054
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c

/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
memory222048000
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
systime0.456
time0.578634977341
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c

/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
memory239040000
return0
status1
stderr
None
stdout
359314 reads; of these:
359314 (100.00%) were unpaired; of these:
46 (0.01%) aligned 0 times
293358 (81.64%) aligned exactly 1 time
65910 (18.34%) aligned >1 times
99.99% overall alignment rate
systime1.576
time27.0296630859
usrtime58.864
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c