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 Mapped29217897.663%
Wrongly Mapped69912.337%
Not Mapped00.0%
Total299169100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome25670.858%
Mapped to wrong position44241.479%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.988200
Precision0.976600
Recall1.000000
Timing
Raw Mapping Time39.180s
Effective Mapping Time38.960s
Effective Init Time0.220s
Effective Time MeasureCPU
Mapping Time (Wall)17.843s
Mapping Time (CPU)39.180s
Mapping Time (CPU User)37.864s
Mapping Time (CPU System)1.316s
Init Time (Wall)0.263s
Init Time (CPU)0.220s
Init Time (CPU User)0.008s
Init Time (CPU System)0.212s
Additional Information
Mapper Memory Usage468 MB
Total Test Runtime (Wall)56.928s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory207432000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.000 CPU sec, 0.001 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.231 sec; CPU: 0.208 sec
systime0.216
time0.251179218292
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory207424000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.000 CPU sec, 0.001 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.238 sec; CPU: 0.208 sec
systime0.212
time0.263058185577
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwamem.sam
memory468356000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 299169 sequences (29916900 bp)...
[M::mem_process_seqs] Processed 299169 reads in 38.268 CPU sec, 9.669 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq
[main] Real time: 17.801 sec; CPU: 39.144 sec
systime1.316
time17.8432319164
usrtime37.864
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c