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 Mapped19623898.392%
Wrongly Mapped32081.608%
Not Mapped00.0%
Total199446100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome9590.481%
Mapped to wrong position22491.128%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.991900
Precision0.983900
Recall1.000000
Timing
Raw Mapping Time47.868s
Effective Mapping Time47.328s
Effective Init Time0.540s
Effective Time MeasureCPU
Mapping Time (Wall)19.340s
Mapping Time (CPU)47.868s
Mapping Time (CPU User)46.472s
Mapping Time (CPU System)1.396s
Init Time (Wall)0.523s
Init Time (CPU)0.540s
Init Time (CPU User)0.168s
Init Time (CPU System)0.372s
Additional Information
Mapper Memory Usage210 MB
Total Test Runtime (Wall)79.180s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/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
memory194632000
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
systime0.496
time13.2715330124
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347

/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
memory194636000
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
systime0.372
time0.522967100143
usrtime0.168
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads.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.fastq -S out_bowtie2.sam
memory210320000
return0
status1
stderr
None
stdout
199446 reads; of these:
199446 (100.00%) were unpaired; of these:
0 (0.00%) aligned 0 times
170026 (85.25%) aligned exactly 1 time
29420 (14.75%) aligned >1 times
100.00% overall alignment rate
systime1.396
time19.3397681713
usrtime46.472
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347