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 Mapped72366280.56%
Wrongly Mapped10986912.231%
Not Mapped647567.209%
Total898287100.0%
Read Failure Statistics
Not mapped647567.209%
Missing in mapper output00.0%
Mapped to wrong chromosome710477.909%
Mapped to wrong position388214.322%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.892300
Precision0.868200
Recall0.917900
Timing
Raw Mapping Time39.420s
Effective Mapping Time38.900s
Effective Init Time0.520s
Effective Time MeasureCPU
Mapping Time (Wall)21.855s
Mapping Time (CPU)39.420s
Mapping Time (CPU User)38.468s
Mapping Time (CPU System)0.952s
Init Time (Wall)0.599s
Init Time (CPU)0.520s
Init Time (CPU User)0.096s
Init Time (CPU System)0.424s
Additional Information
Mapper Memory Usage322 MB
Total Test Runtime (Wall)131.968s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads.fastq out_bowtie.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads_base.fastq out_bowtie.sam
memory322456000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime0.572
time11.5207400322
usrtime0.06
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads_base.fastq out_bowtie.sam
memory322456000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime0.424
time0.599263906479
usrtime0.096
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads.fastq out_bowtie.sam
memory322456000
return0
status1
stderr
None
stdout
# reads processed: 898287
# reads with at least one reported alignment: 833531 (92.79%)
# reads that failed to align: 64756 (7.21%)
Reported 833531 alignments to 1 output stream(s)
systime0.952
time21.8554029465
usrtime38.468
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef