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 Mapped29254897.516%
Wrongly Mapped51001.7%
Not Mapped23520.784%
Total300000100.0%
Read Failure Statistics
Not mapped23520.784%
Missing in mapper output00.0%
Mapped to wrong chromosome41261.375%
Mapped to wrong position9740.325%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.987400
Precision0.982900
Recall0.992000
Timing
Raw Mapping Time38.164s
Effective Mapping Time37.708s
Effective Init Time0.456s
Effective Time MeasureCPU
Mapping Time (Wall)18.752s
Mapping Time (CPU)38.164s
Mapping Time (CPU User)37.104s
Mapping Time (CPU System)1.060s
Init Time (Wall)0.628s
Init Time (CPU)0.456s
Init Time (CPU User)0.148s
Init Time (CPU System)0.308s
Additional Information
Mapper Memory Usage79 MB
Total Test Runtime (Wall)75.328s
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
memory58964000
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
time4.35568785667
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/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
memory70516000
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
time0.628056049347
usrtime0.148
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/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
memory79024000
return0
status1
stderr
None
stdout
300000 reads; of these:
300000 (100.00%) were unpaired; of these:
2352 (0.78%) aligned 0 times
286030 (95.34%) aligned exactly 1 time
11618 (3.87%) aligned >1 times
99.22% overall alignment rate
systime1.06
time18.7521510124
usrtime37.104
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972