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 Mapped68747587.656%
Wrongly Mapped8097210.324%
Not Mapped158432.02%
Total784290100.0%
Read Failure Statistics
Not mapped158432.02%
Missing in mapper output00.0%
Mapped to wrong chromosome660968.427%
Mapped to wrong position148731.896%
Mapped to wrong strand30.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.934200
Precision0.894600
Recall0.977500
Timing
Raw Mapping Time103.944s
Effective Mapping Time100.196s
Effective Init Time3.748s
Effective Time MeasureCPU
Mapping Time (Wall)41.187s
Mapping Time (CPU)103.944s
Mapping Time (CPU User)97.608s
Mapping Time (CPU System)6.336s
Init Time (Wall)3.726s
Init Time (CPU)3.748s
Init Time (CPU User)0.120s
Init Time (CPU System)3.628s
Additional Information
Mapper Memory Usage3380 MB
Total Test Runtime (Wall)455.835s
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
memory3361572000
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
systime4.528
time289.332525015
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd

/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
memory3358920000
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
systime3.628
time3.7260620594
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd

/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
memory3380244000
return0
status1
stderr
None
stdout
784290 reads; of these:
784290 (100.00%) were unpaired; of these:
15843 (2.02%) aligned 0 times
578764 (73.79%) aligned exactly 1 time
189683 (24.19%) aligned >1 times
97.98% overall alignment rate
systime6.336
time41.1866250038
usrtime97.608
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd