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 Mapped9903299.032%
Wrongly Mapped7670.767%
Not Mapped2010.201%
Total100000100.0%
Read Failure Statistics
Not mapped2010.201%
Missing in mapper output00.0%
Mapped to wrong chromosome5240.524%
Mapped to wrong position2430.243%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.995100
Precision0.992300
Recall0.998000
Timing
Raw Mapping Time35.316s
Effective Mapping Time34.876s
Effective Init Time0.440s
Effective Time MeasureCPU
Mapping Time (Wall)15.216s
Mapping Time (CPU)35.316s
Mapping Time (CPU User)34.156s
Mapping Time (CPU System)1.160s
Init Time (Wall)0.410s
Init Time (CPU)0.440s
Init Time (CPU User)0.096s
Init Time (CPU System)0.344s
Additional Information
Mapper Memory Usage101 MB
Total Test Runtime (Wall)56.805s
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
memory73804000
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
systime0.3
time0.351151943207
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3

/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
memory71840000
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
systime0.344
time0.409678936005
usrtime0.096
working_directory/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3

/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
memory101372000
return0
status1
stderr
None
stdout
50000 reads; of these:
50000 (100.00%) were paired; of these:
181 (0.36%) aligned concordantly 0 times
48412 (96.82%) aligned concordantly exactly 1 time
1407 (2.81%) aligned concordantly >1 times
----
181 pairs aligned concordantly 0 times; of these:
75 (41.44%) aligned discordantly 1 time
----
106 pairs aligned 0 times concordantly or discordantly; of these:
212 mates make up the pairs; of these:
201 (94.81%) aligned 0 times
3 (1.42%) aligned exactly 1 time
8 (3.77%) aligned >1 times
99.80% overall alignment rate
systime1.16
time15.2161109447
usrtime34.156
working_directory/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3