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 Mapped24654298.617%
Wrongly Mapped32701.308%
Not Mapped1880.075%
Total250000100.0%
Read Failure Statistics
Not mapped1880.075%
Missing in mapper output00.0%
Mapped to wrong chromosome25061.002%
Mapped to wrong position7640.306%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.993000
Precision0.986900
Recall0.999200
Timing
Raw Mapping Time30.088s
Effective Mapping Time29.844s
Effective Init Time0.244s
Effective Time MeasureCPU
Mapping Time (Wall)8.854s
Mapping Time (CPU)30.088s
Mapping Time (CPU User)29.709s
Mapping Time (CPU System)0.379s
Init Time (Wall)0.220s
Init Time (CPU)0.244s
Init Time (CPU User)0.045s
Init Time (CPU System)0.199s
Additional Information
Mapper Memory Usage86 MB
Total Test Runtime (Wall)24.395s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_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/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory62652000
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
systime0.175973
time0.575767040253
usrtime0.044993
working_directory/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory58460000
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
systime0.198969
time0.219805002213
usrtime0.044993
working_directory/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_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/Saccharomyces_cerevisiae.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory86124000
return0
status1
stderr
None
stdout
125000 reads; of these:
125000 (100.00%) were paired; of these:
14409 (11.53%) aligned concordantly 0 times
106514 (85.21%) aligned concordantly exactly 1 time
4077 (3.26%) aligned concordantly >1 times
----
14409 pairs aligned concordantly 0 times; of these:
13714 (95.18%) aligned discordantly 1 time
----
695 pairs aligned 0 times concordantly or discordantly; of these:
1390 mates make up the pairs; of these:
188 (13.53%) aligned 0 times
28 (2.01%) aligned exactly 1 time
1174 (84.46%) aligned >1 times
99.92% overall alignment rate
systime0.378942
time8.85408592224
usrtime29.709483
working_directory/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943