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 Mapped57238995.663%
Wrongly Mapped252214.215%
Not Mapped7280.122%
Total598338100.0%
Read Failure Statistics
Not mapped7280.122%
Missing in mapper output00.0%
Mapped to wrong chromosome122322.044%
Mapped to wrong position129892.171%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.977800
Precision0.957800
Recall0.998700
Timing
Raw Mapping Time102.212s
Effective Mapping Time93.900s
Effective Init Time8.312s
Effective Time MeasureCPU
Mapping Time (Wall)44.254s
Mapping Time (CPU)102.212s
Mapping Time (CPU User)86.668s
Mapping Time (CPU System)15.544s
Init Time (Wall)8.528s
Init Time (CPU)8.312s
Init Time (CPU User)0.008s
Init Time (CPU System)8.304s
Additional Information
Mapper Memory Usage568 MB
Total Test Runtime (Wall)140.092s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory207404000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.104 CPU sec, 0.102 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 9.122 sec; CPU: 8.908 sec
systime8.916
time9.25152397156
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory207404000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.076 CPU sec, 0.076 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 8.483 sec; CPU: 8.296 sec
systime8.304
time8.52758908272
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwamem.sam
memory568588000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 598338 sequences (29916900 bp)...
[M::mem_process_seqs] Processed 598338 reads in 90.880 CPU sec, 23.474 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq
[main] Real time: 44.202 sec; CPU: 102.172 sec
systime15.544
time44.2539181709
usrtime86.668
working_directory/project/teaser/genometeaser/tests_generated/0542e1134664dca94011ee7ee39d31ff