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 Mapped17475998.164%
Wrongly Mapped32231.81%
Not Mapped460.026%
Total178028100.0%
Read Failure Statistics
Not mapped460.026%
Missing in mapper output00.0%
Mapped to wrong chromosome23961.346%
Mapped to wrong position8270.465%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.990700
Precision0.981900
Recall0.999700
Timing
Raw Mapping Time140.296s
Effective Mapping Time137.776s
Effective Init Time2.520s
Effective Time MeasureCPU
Mapping Time (Wall)41.910s
Mapping Time (CPU)140.296s
Mapping Time (CPU User)130.716s
Mapping Time (CPU System)9.580s
Init Time (Wall)2.981s
Init Time (CPU)2.520s
Init Time (CPU User)0.164s
Init Time (CPU System)2.356s
Additional Information
Mapper Memory Usage3136 MB
Total Test Runtime (Wall)358.428s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Bos_taurus.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/Bos_taurus.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Bos_taurus.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3081880000
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
systime4.24
time283.712658167
usrtime0.144
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Bos_taurus.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3081916000
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
systime2.356
time2.98063111305
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Bos_taurus.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/Bos_taurus.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory3136660000
return0
status1
stderr
None
stdout
89014 reads; of these:
89014 (100.00%) were paired; of these:
82733 (92.94%) aligned concordantly 0 times
5194 (5.84%) aligned concordantly exactly 1 time
1087 (1.22%) aligned concordantly >1 times
----
82733 pairs aligned concordantly 0 times; of these:
67609 (81.72%) aligned discordantly 1 time
----
15124 pairs aligned 0 times concordantly or discordantly; of these:
30248 mates make up the pairs; of these:
46 (0.15%) aligned 0 times
3288 (10.87%) aligned exactly 1 time
26914 (88.98%) aligned >1 times
99.97% overall alignment rate
systime9.58
time41.9104630947
usrtime130.716
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567