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 Mapped51419485.862%
Wrongly Mapped6935511.581%
Not Mapped153092.556%
Total598858100.0%
Read Failure Statistics
Not mapped153092.556%
Missing in mapper output00.0%
Mapped to wrong chromosome434217.251%
Mapped to wrong position259344.331%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment43
Secondary Alignments0
F-Measure0.923900
Precision0.881100
Recall0.971100
Timing
Raw Mapping Time219.184s
Effective Mapping Time217.796s
Effective Init Time1.388s
Effective Time MeasureCPU
Mapping Time (Wall)71.528s
Mapping Time (CPU)219.184s
Mapping Time (CPU User)208.216s
Mapping Time (CPU System)10.968s
Init Time (Wall)1.456s
Init Time (CPU)1.388s
Init Time (CPU User)0.000s
Init Time (CPU System)1.388s
Additional Information
Mapper Memory Usage684 MB
Total Test Runtime (Wall)122.458s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248992000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 1.049 sec; CPU: 0.988 sec
systime0.992
time1.07427501678
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248992000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 1.429 sec; CPU: 1.376 sec
systime1.388
time1.45623612404
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
memory684876000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 598858 sequences/pairs (35931480 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 71.476 sec; CPU: 219.128 sec
systime10.968
time71.5280511379
usrtime208.216
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8