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 Mapped58693374.836%
Wrongly Mapped748069.538%
Not Mapped12255115.626%
Total784290100.0%
Read Failure Statistics
Not mapped12255115.626%
Missing in mapper output00.0%
Mapped to wrong chromosome621507.924%
Mapped to wrong position126531.613%
Mapped to wrong strand30.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.856100
Precision0.887000
Recall0.827300
Timing
Raw Mapping Time213.868s
Effective Mapping Time209.416s
Effective Init Time4.452s
Effective Time MeasureCPU
Mapping Time (Wall)97.887s
Mapping Time (CPU)213.868s
Mapping Time (CPU User)193.968s
Mapping Time (CPU System)19.900s
Init Time (Wall)4.512s
Init Time (CPU)4.452s
Init Time (CPU User)0.112s
Init Time (CPU System)4.340s
Additional Information
Mapper Memory Usage5884 MB
Total Test Runtime (Wall)187.638s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366548000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.446 sec; CPU: 4.388 sec
systime4.3
time4.46828794479
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366684000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.484 sec; CPU: 4.432 sec
systime4.34
time4.51200389862
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
memory5884064000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 784290 sequences/pairs (31371600 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq
[main] Real time: 97.814 sec; CPU: 213.852 sec
systime19.9
time97.8873970509
usrtime193.968
working_directory/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd