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 Mapped44227391.409%
Wrongly Mapped412978.535%
Not Mapped2720.056%
Total483842100.0%
Read Failure Statistics
Not mapped2720.056%
Missing in mapper output00.0%
Mapped to wrong chromosome213724.417%
Mapped to wrong position199254.118%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.955100
Precision0.914600
Recall0.999400
Timing
Raw Mapping Time425.384s
Effective Mapping Time395.880s
Effective Init Time29.504s
Effective Time MeasureCPU
Mapping Time (Wall)168.617s
Mapping Time (CPU)425.384s
Mapping Time (CPU User)379.252s
Mapping Time (CPU System)46.132s
Init Time (Wall)30.529s
Init Time (CPU)29.504s
Init Time (CPU User)0.060s
Init Time (CPU System)29.444s
Additional Information
Mapper Memory Usage3161 MB
Total Test Runtime (Wall)573.664s
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
memory3086872000
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
systime29.0
time266.496309042
usrtime0.076
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8

/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
memory3080004000
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
systime29.444
time30.529184103
usrtime0.06
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8

/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
memory3161652000
return0
status1
stderr
None
stdout
483842 reads; of these:
483842 (100.00%) were unpaired; of these:
272 (0.06%) aligned 0 times
381423 (78.83%) aligned exactly 1 time
102147 (21.11%) aligned >1 times
99.94% overall alignment rate
systime46.132
time168.617214918
usrtime379.252
working_directory/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8