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 Mapped52797188.163%
Wrongly Mapped6896311.516%
Not Mapped19240.321%
Total598858100.0%
Read Failure Statistics
Not mapped19240.321%
Missing in mapper output00.0%
Mapped to wrong chromosome415346.936%
Mapped to wrong position274294.58%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937100
Precision0.884500
Recall0.996400
Timing
Raw Mapping Time99.388s
Effective Mapping Time97.568s
Effective Init Time1.820s
Effective Time MeasureCPU
Mapping Time (Wall)37.956s
Mapping Time (CPU)99.388s
Mapping Time (CPU User)94.204s
Mapping Time (CPU System)5.184s
Init Time (Wall)1.866s
Init Time (CPU)1.820s
Init Time (CPU User)0.108s
Init Time (CPU System)1.712s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)175.199s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory221204000
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
systime1.948
time15.740049839
usrtime0.128
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory220208000
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
systime1.712
time1.86580014229
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory236408000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1924 (0.32%) aligned 0 times
486055 (81.16%) aligned exactly 1 time
110879 (18.52%) aligned >1 times
99.68% overall alignment rate
systime5.184
time37.9564590454
usrtime94.204
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3