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 Mapped70955687.99%
Wrongly Mapped9384611.638%
Not Mapped30020.372%
Total806404100.0%
Read Failure Statistics
Not mapped30020.372%
Missing in mapper output00.0%
Mapped to wrong chromosome550156.822%
Mapped to wrong position388304.815%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936100
Precision0.883200
Recall0.995800
Timing
Raw Mapping Time366.692s
Effective Mapping Time362.940s
Effective Init Time3.752s
Effective Time MeasureCPU
Mapping Time (Wall)95.940s
Mapping Time (CPU)366.692s
Mapping Time (CPU User)360.444s
Mapping Time (CPU System)6.248s
Init Time (Wall)3.727s
Init Time (CPU)3.752s
Init Time (CPU User)0.116s
Init Time (CPU System)3.636s
Additional Information
Mapper Memory Usage3156 MB
Total Test Runtime (Wall)498.335s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.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/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3088236000
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
systime5.808
time265.992847204
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3088904000
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
systime3.636
time3.72659397125
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory3156484000
return0
status1
stderr
None
stdout
806404 reads; of these:
806404 (100.00%) were unpaired; of these:
3002 (0.37%) aligned 0 times
612633 (75.97%) aligned exactly 1 time
190769 (23.66%) aligned >1 times
99.63% overall alignment rate
systime6.248
time95.9400861263
usrtime360.444
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31