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 Mapped52841288.237%
Wrongly Mapped6853811.445%
Not Mapped19080.319%
Total598858100.0%
Read Failure Statistics
Not mapped19080.319%
Missing in mapper output00.0%
Mapped to wrong chromosome409406.836%
Mapped to wrong position275984.608%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937500
Precision0.885200
Recall0.996400
Timing
Raw Mapping Time74.648s
Effective Mapping Time74.056s
Effective Init Time0.592s
Effective Time MeasureCPU
Mapping Time (Wall)31.198s
Mapping Time (CPU)74.648s
Mapping Time (CPU User)72.456s
Mapping Time (CPU System)2.192s
Init Time (Wall)0.568s
Init Time (CPU)0.592s
Init Time (CPU User)0.148s
Init Time (CPU System)0.444s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)152.372s
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
memory224320000
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
systime0.508
time16.3510780334
usrtime0.144
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b

/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
memory222048000
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
systime0.444
time0.568197011948
usrtime0.148
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b

/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
memory236288000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1908 (0.32%) aligned 0 times
485465 (81.07%) aligned exactly 1 time
111485 (18.62%) aligned >1 times
99.68% overall alignment rate
systime2.192
time31.1983160973
usrtime72.456
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b