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 Mapped29239897.466%
Wrongly Mapped52191.74%
Not Mapped23830.794%
Total300000100.0%
Read Failure Statistics
Not mapped23830.794%
Missing in mapper output00.0%
Mapped to wrong chromosome42551.418%
Mapped to wrong position9640.321%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.987200
Precision0.982500
Recall0.991900
Timing
Raw Mapping Time66.956s
Effective Mapping Time66.604s
Effective Init Time0.352s
Effective Time MeasureCPU
Mapping Time (Wall)145.125s
Mapping Time (CPU)66.956s
Mapping Time (CPU User)45.340s
Mapping Time (CPU System)21.616s
Init Time (Wall)41.406s
Init Time (CPU)0.352s
Init Time (CPU User)0.112s
Init Time (CPU System)0.240s
Additional Information
Mapper Memory Usage81 MB
Total Test Runtime (Wall)380.022s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_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/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
memory62008000
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
systime0.292
time7.68317699432
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f

/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
memory72568000
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
systime0.24
time41.406471014
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads.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.fastq -S out_bowtie2.sam
memory81164000
return0
status1
stderr
None
stdout
300000 reads; of these:
300000 (100.00%) were unpaired; of these:
2383 (0.79%) aligned 0 times
285555 (95.19%) aligned exactly 1 time
12062 (4.02%) aligned >1 times
99.21% overall alignment rate
systime21.616
time145.124502897
usrtime45.34
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f