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 Mapped30057795.813%
Wrongly Mapped111763.562%
Not Mapped19600.625%
Total313713100.0%
Read Failure Statistics
Not mapped19600.625%
Missing in mapper output00.0%
Mapped to wrong chromosome79302.528%
Mapped to wrong position32461.035%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments0
F-Measure0.978600
Precision0.964200
Recall0.993500
Timing
Raw Mapping Time175.450s
Effective Mapping Time173.123s
Effective Init Time2.328s
Effective Time MeasureCPU
Mapping Time (Wall)46.056s
Mapping Time (CPU)175.450s
Mapping Time (CPU User)172.809s
Mapping Time (CPU System)2.642s
Init Time (Wall)7.817s
Init Time (CPU)2.328s
Init Time (CPU User)0.054s
Init Time (CPU System)2.274s
Additional Information
Mapper Memory Usage3400 MB
Total Test Runtime (Wall)103.134s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.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
memory3347452000
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
systime3.35049
time29.4579379559
usrtime0.049992
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/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
memory3346180000
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
systime2.273654
time7.81714010239
usrtime0.053991
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory3400640000
return0
status1
stderr
None
stdout
156858 reads; of these:
156858 (100.00%) were paired; of these:
1148 (0.73%) aligned concordantly 0 times
130001 (82.88%) aligned concordantly exactly 1 time
25709 (16.39%) aligned concordantly >1 times
----
1148 pairs aligned concordantly 0 times; of these:
2 (0.17%) aligned discordantly 1 time
----
1146 pairs aligned 0 times concordantly or discordantly; of these:
2292 mates make up the pairs; of these:
1962 (85.60%) aligned 0 times
46 (2.01%) aligned exactly 1 time
284 (12.39%) aligned >1 times
99.37% overall alignment rate
systime2.641598
time46.0562889576
usrtime172.808729
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3