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 Mapped9858498.584%
Wrongly Mapped11861.186%
Not Mapped2300.23%
Total100000100.0%
Read Failure Statistics
Not mapped2300.23%
Missing in mapper output00.0%
Mapped to wrong chromosome9700.97%
Mapped to wrong position2160.216%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.992900
Precision0.988100
Recall0.997700
Timing
Raw Mapping Time43.740s
Effective Mapping Time43.456s
Effective Init Time0.284s
Effective Time MeasureCPU
Mapping Time (Wall)17.308s
Mapping Time (CPU)43.740s
Mapping Time (CPU User)42.680s
Mapping Time (CPU System)1.060s
Init Time (Wall)0.644s
Init Time (CPU)0.284s
Init Time (CPU User)0.080s
Init Time (CPU System)0.204s
Additional Information
Mapper Memory Usage102 MB
Total Test Runtime (Wall)62.228s
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
memory63312000
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
systime0.308
time3.9229581356
usrtime0.084
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

/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
memory60812000
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
systime0.204
time0.643585920334
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9

/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
memory102136000
return0
status1
stderr
None
stdout
50000 reads; of these:
50000 (100.00%) were paired; of these:
46249 (92.50%) aligned concordantly 0 times
3598 (7.20%) aligned concordantly exactly 1 time
153 (0.31%) aligned concordantly >1 times
----
46249 pairs aligned concordantly 0 times; of these:
44306 (95.80%) aligned discordantly 1 time
----
1943 pairs aligned 0 times concordantly or discordantly; of these:
3886 mates make up the pairs; of these:
230 (5.92%) aligned 0 times
152 (3.91%) aligned exactly 1 time
3504 (90.17%) aligned >1 times
99.77% overall alignment rate
systime1.06
time17.3084609509
usrtime42.68
working_directory/project/teaser/genometeaser/tests_generated/b0bfc21db96b7744c4389e9b4b565dc9