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 Mapped9899198.991%
Wrongly Mapped7760.776%
Not Mapped2330.233%
Total100000100.0%
Read Failure Statistics
Not mapped2330.233%
Missing in mapper output00.0%
Mapped to wrong chromosome5680.568%
Mapped to wrong position2080.208%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.994900
Precision0.992200
Recall0.997700
Timing
Raw Mapping Time39.172s
Effective Mapping Time38.776s
Effective Init Time0.396s
Effective Time MeasureCPU
Mapping Time (Wall)15.791s
Mapping Time (CPU)39.172s
Mapping Time (CPU User)36.120s
Mapping Time (CPU System)3.052s
Init Time (Wall)2.668s
Init Time (CPU)0.396s
Init Time (CPU User)0.152s
Init Time (CPU System)0.244s
Additional Information
Mapper Memory Usage109 MB
Total Test Runtime (Wall)44.450s
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
memory72100000
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
systime0.288
time0.38770198822
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f

/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
memory73960000
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
systime0.244
time2.66806507111
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f

/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
memory109416000
return0
status1
stderr
None
stdout
50000 reads; of these:
50000 (100.00%) were paired; of these:
177 (0.35%) aligned concordantly 0 times
48303 (96.61%) aligned concordantly exactly 1 time
1520 (3.04%) aligned concordantly >1 times
----
177 pairs aligned concordantly 0 times; of these:
57 (32.20%) aligned discordantly 1 time
----
120 pairs aligned 0 times concordantly or discordantly; of these:
240 mates make up the pairs; of these:
233 (97.08%) aligned 0 times
4 (1.67%) aligned exactly 1 time
3 (1.25%) aligned >1 times
99.77% overall alignment rate
systime3.052
time15.7905089855
usrtime36.12
working_directory/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f