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 Mapped19622898.387%
Wrongly Mapped32181.613%
Not Mapped00.0%
Total199446100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome9760.489%
Mapped to wrong position22421.124%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.991900
Precision0.983900
Recall1.000000
Timing
Raw Mapping Time38.804s
Effective Mapping Time38.588s
Effective Init Time0.216s
Effective Time MeasureCPU
Mapping Time (Wall)16.982s
Mapping Time (CPU)38.804s
Mapping Time (CPU User)38.076s
Mapping Time (CPU System)0.728s
Init Time (Wall)0.260s
Init Time (CPU)0.216s
Init Time (CPU User)0.012s
Init Time (CPU System)0.204s
Additional Information
Mapper Memory Usage402 MB
Total Test Runtime (Wall)49.103s
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
memory207336000
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 0.004 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: 0.259 sec; CPU: 0.208 sec
systime0.208
time0.28089594841
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347

/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
memory209224000
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 0.004 CPU sec, 0.002 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: 0.233 sec; CPU: 0.208 sec
systime0.204
time0.260108947754
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347

/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
memory402068000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 199446 sequences (29916900 bp)...
[M::mem_process_seqs] Processed 199446 reads in 37.896 CPU sec, 9.490 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: 16.947 sec; CPU: 38.796 sec
systime0.728
time16.9820809364
usrtime38.076
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347