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 Mapped49149594.001%
Wrongly Mapped312775.982%
Not Mapped880.017%
Total522860100.0%
Read Failure Statistics
Not mapped880.017%
Missing in mapper output00.0%
Mapped to wrong chromosome231914.435%
Mapped to wrong position80851.546%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments1
F-Measure0.969100
Precision0.940200
Recall0.999800
Timing
Raw Mapping Time144.112s
Effective Mapping Time139.672s
Effective Init Time4.440s
Effective Time MeasureCPU
Mapping Time (Wall)49.693s
Mapping Time (CPU)144.112s
Mapping Time (CPU User)135.636s
Mapping Time (CPU System)8.476s
Init Time (Wall)4.503s
Init Time (CPU)4.440s
Init Time (CPU User)0.132s
Init Time (CPU System)4.308s
Additional Information
Mapper Memory Usage6195 MB
Total Test Runtime (Wall)119.130s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa 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/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5364628000
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 0.068 CPU sec, 0.064 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.474 sec; CPU: 4.420 sec
systime4.332
time4.52888607979
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5365820000
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 0.064 CPU sec, 0.061 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.472 sec; CPU: 4.424 sec
systime4.308
time4.50294208527
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwamem.sam
memory6195852000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 522860 sequences (31371600 bp)...
[M::mem_process_seqs] Processed 522860 reads in 138.976 CPU sec, 35.372 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq
[main] Real time: 49.646 sec; CPU: 144.100 sec
systime8.476
time49.6925559044
usrtime135.636
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8