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 Mapped53864490.023%
Wrongly Mapped241964.044%
Not Mapped354985.933%
Total598338100.0%
Read Failure Statistics
Not mapped354985.933%
Missing in mapper output00.0%
Mapped to wrong chromosome119802.002%
Mapped to wrong position122162.042%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment1
Secondary Alignments0
F-Measure0.947500
Precision0.957000
Recall0.938200
Timing
Raw Mapping Time341.236s
Effective Mapping Time331.216s
Effective Init Time10.020s
Effective Time MeasureCPU
Mapping Time (Wall)104.139s
Mapping Time (CPU)341.236s
Mapping Time (CPU User)319.108s
Mapping Time (CPU System)22.128s
Init Time (Wall)10.256s
Init Time (CPU)10.020s
Init Time (CPU User)0.008s
Init Time (CPU System)10.012s
Additional Information
Mapper Memory Usage623 MB
Total Test Runtime (Wall)197.403s
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
memory207884000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 9.927 sec; CPU: 9.724 sec
systime9.736
time9.95854616165
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff

/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
memory207880000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 10.226 sec; CPU: 10.004 sec
systime10.012
time10.2564918995
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff

/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
memory623036000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 598338 sequences/pairs (29916900 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq
[main] Real time: 104.100 sec; CPU: 341.204 sec
systime22.128
time104.138942003
usrtime319.108
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff