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 Mapped48822993.377%
Wrongly Mapped324976.215%
Not Mapped21340.408%
Total522860100.0%
Read Failure Statistics
Not mapped21340.408%
Missing in mapper output00.0%
Mapped to wrong chromosome243584.659%
Mapped to wrong position81391.557%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.965700
Precision0.937600
Recall0.995600
Timing
Raw Mapping Time152.944s
Effective Mapping Time149.208s
Effective Init Time3.736s
Effective Time MeasureCPU
Mapping Time (Wall)45.212s
Mapping Time (CPU)152.944s
Mapping Time (CPU User)147.280s
Mapping Time (CPU System)5.664s
Init Time (Wall)3.756s
Init Time (CPU)3.736s
Init Time (CPU User)0.124s
Init Time (CPU System)3.612s
Additional Information
Mapper Memory Usage3386 MB
Total Test Runtime (Wall)433.033s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_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/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359416000
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
systime4.472
time289.403796911
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359360000
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
systime3.612
time3.75610995293
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam
memory3386144000
return0
status1
stderr
None
stdout
522860 reads; of these:
522860 (100.00%) were unpaired; of these:
2134 (0.41%) aligned 0 times
409175 (78.26%) aligned exactly 1 time
111551 (21.33%) aligned >1 times
99.59% overall alignment rate
systime5.664
time45.211605072
usrtime147.28
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8