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 Mapped9824898.248%
Wrongly Mapped17521.752%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome8940.894%
Mapped to wrong position8580.858%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.991200
Precision0.982500
Recall1.000000
Timing
Raw Mapping Time50.320s
Effective Mapping Time48.416s
Effective Init Time1.904s
Effective Time MeasureCPU
Mapping Time (Wall)17.672s
Mapping Time (CPU)50.320s
Mapping Time (CPU User)47.504s
Mapping Time (CPU System)2.816s
Init Time (Wall)1.918s
Init Time (CPU)1.904s
Init Time (CPU User)0.392s
Init Time (CPU System)1.512s
Additional Information
Mapper Memory Usage1286 MB
Total Test Runtime (Wall)148.141s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Gallus_gallus.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/Gallus_gallus.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Gallus_gallus.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory1247468000
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
systime1.844
time105.00875783
usrtime0.376
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Gallus_gallus.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory1247744000
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
systime1.512
time1.91782593727
usrtime0.392
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Gallus_gallus.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/Gallus_gallus.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory1286376000
return0
status1
stderr
None
stdout
50000 reads; of these:
50000 (100.00%) were paired; of these:
49948 (99.90%) aligned concordantly 0 times
17 (0.03%) aligned concordantly exactly 1 time
35 (0.07%) aligned concordantly >1 times
----
49948 pairs aligned concordantly 0 times; of these:
46689 (93.48%) aligned discordantly 1 time
----
3259 pairs aligned 0 times concordantly or discordantly; of these:
6518 mates make up the pairs; of these:
0 (0.00%) aligned 0 times
395 (6.06%) aligned exactly 1 time
6123 (93.94%) aligned >1 times
100.00% overall alignment rate
systime2.816
time17.6722249985
usrtime47.504
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a