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 Mapped19566198.102%
Wrongly Mapped37841.897%
Not Mapped10.001%
Total199446100.0%
Read Failure Statistics
Not mapped10.001%
Missing in mapper output00.0%
Mapped to wrong chromosome10870.545%
Mapped to wrong position26971.352%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.990400
Precision0.981000
Recall1.000000
Timing
Raw Mapping Time127.916s
Effective Mapping Time127.364s
Effective Init Time0.552s
Effective Time MeasureCPU
Mapping Time (Wall)52.777s
Mapping Time (CPU)127.916s
Mapping Time (CPU User)125.412s
Mapping Time (CPU System)2.504s
Init Time (Wall)0.728s
Init Time (CPU)0.552s
Init Time (CPU User)0.088s
Init Time (CPU System)0.464s
Additional Information
Mapper Memory Usage228 MB
Total Test Runtime (Wall)144.115s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory193680000
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
systime0.456
time18.1091790199
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory194104000
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
systime0.464
time0.728059053421
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory228464000
return0
status1
stderr
None
stdout
99723 reads; of these:
99723 (100.00%) were paired; of these:
92465 (92.72%) aligned concordantly 0 times
5901 (5.92%) aligned concordantly exactly 1 time
1357 (1.36%) aligned concordantly >1 times
----
92465 pairs aligned concordantly 0 times; of these:
77575 (83.90%) aligned discordantly 1 time
----
14890 pairs aligned 0 times concordantly or discordantly; of these:
29780 mates make up the pairs; of these:
1 (0.00%) aligned 0 times
2519 (8.46%) aligned exactly 1 time
27260 (91.54%) aligned >1 times
100.00% overall alignment rate
systime2.504
time52.7769019604
usrtime125.412
working_directory/project/teaser/genometeaser/tests_generated/e1c9b59d61d1a772598b0749ea6b7508