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 Mapped53060688.603%
Wrongly Mapped6815011.38%
Not Mapped1020.017%
Total598858100.0%
Read Failure Statistics
Not mapped1020.017%
Missing in mapper output00.0%
Mapped to wrong chromosome402696.724%
Mapped to wrong position278814.656%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.939600
Precision0.886200
Recall0.999800
Timing
Raw Mapping Time190.588s
Effective Mapping Time189.980s
Effective Init Time0.608s
Effective Time MeasureCPU
Mapping Time (Wall)130.466s
Mapping Time (CPU)190.588s
Mapping Time (CPU User)180.052s
Mapping Time (CPU System)10.536s
Init Time (Wall)0.622s
Init Time (CPU)0.608s
Init Time (CPU User)0.032s
Init Time (CPU System)0.576s
Additional Information
Mapper Memory Usage884 MB
Total Test Runtime (Wall)216.848s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory250620000
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, 0.005 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.829 sec; CPU: 0.592 sec
systime0.596
time0.852111816406
usrtime0.028
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248780000
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, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.607 sec; CPU: 0.584 sec
systime0.576
time0.622362852097
usrtime0.032
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
memory884500000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 598858 sequences (35931480 bp)...
[M::mem_process_seqs] Processed 598858 reads in 187.628 CPU sec, 106.020 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 130.403 sec; CPU: 190.564 sec
systime10.536
time130.466248989
usrtime180.052
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587