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 Mapped39956895.622%
Wrongly Mapped169924.066%
Not Mapped13000.311%
Total417860100.0%
Read Failure Statistics
Not mapped13000.311%
Missing in mapper output00.0%
Mapped to wrong chromosome64111.534%
Mapped to wrong position105802.532%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.977600
Precision0.959200
Recall0.996800
Timing
Raw Mapping Time64.856s
Effective Mapping Time64.356s
Effective Init Time0.500s
Effective Time MeasureCPU
Mapping Time (Wall)24.579s
Mapping Time (CPU)64.856s
Mapping Time (CPU User)62.864s
Mapping Time (CPU System)1.992s
Init Time (Wall)0.498s
Init Time (CPU)0.500s
Init Time (CPU User)0.124s
Init Time (CPU System)0.376s
Additional Information
Mapper Memory Usage183 MB
Total Test Runtime (Wall)108.620s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/C_elegans.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/C_elegans.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/C_elegans.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory174764000
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
systime0.452
time11.8145070076
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/C_elegans.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory172868000
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
systime0.376
time0.498481035233
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/C_elegans.fa_bt -U reads.fastq -S out_bowtie2.sam
memory183948000
return0
status1
stderr
None
stdout
417860 reads; of these:
417860 (100.00%) were unpaired; of these:
1300 (0.31%) aligned 0 times
365515 (87.47%) aligned exactly 1 time
51045 (12.22%) aligned >1 times
99.69% overall alignment rate
systime1.992
time24.5794789791
usrtime62.864
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6