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 Mapped19613198.338%
Wrongly Mapped33141.662%
Not Mapped10.001%
Total199446100.0%
Read Failure Statistics
Not mapped10.001%
Missing in mapper output00.0%
Mapped to wrong chromosome10270.515%
Mapped to wrong position22871.147%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment1
Secondary Alignments0
F-Measure0.991600
Precision0.983400
Recall1.000000
Timing
Raw Mapping Time230.816s
Effective Mapping Time230.600s
Effective Init Time0.216s
Effective Time MeasureCPU
Mapping Time (Wall)84.389s
Mapping Time (CPU)230.816s
Mapping Time (CPU User)226.724s
Mapping Time (CPU System)4.092s
Init Time (Wall)0.270s
Init Time (CPU)0.216s
Init Time (CPU User)0.008s
Init Time (CPU System)0.208s
Additional Information
Mapper Memory Usage446 MB
Total Test Runtime (Wall)116.625s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory207604000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.156 sec; CPU: 0.132 sec
systime0.132
time0.176414012909
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory207728000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.241 sec; CPU: 0.208 sec
systime0.208
time0.270256996155
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwasw.sam
memory446512000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 199446 sequences/pairs (29916900 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq
[main] Real time: 84.352 sec; CPU: 230.808 sec
systime4.092
time84.3889141083
usrtime226.724
working_directory/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347