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 Mapped28045593.485%
Wrongly Mapped50251.675%
Not Mapped145204.84%
Total300000100.0%
Read Failure Statistics
Not mapped145204.84%
Missing in mapper output00.0%
Mapped to wrong chromosome40681.356%
Mapped to wrong position9570.319%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.966300
Precision0.982400
Recall0.950800
Timing
Raw Mapping Time153.468s
Effective Mapping Time153.368s
Effective Init Time0.100s
Effective Time MeasureCPU
Mapping Time (Wall)76.841s
Mapping Time (CPU)153.468s
Mapping Time (CPU User)146.264s
Mapping Time (CPU System)7.204s
Init Time (Wall)0.419s
Init Time (CPU)0.100s
Init Time (CPU User)0.020s
Init Time (CPU System)0.080s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)156.764s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.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/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory48836000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.105 sec; CPU: 0.048 sec
systime0.048
time0.330631017685
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory48836000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.170 sec; CPU: 0.084 sec
systime0.08
time0.419489145279
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq -t 4 > out_bwasw.sam
memory236460000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 300000 sequences/pairs (15000000 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq
[main] Real time: 76.780 sec; CPU: 153.436 sec
systime7.204
time76.8411078453
usrtime146.264
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f