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 Mapped40082395.923%
Wrongly Mapped169814.064%
Not Mapped560.013%
Total417860100.0%
Read Failure Statistics
Not mapped560.013%
Missing in mapper output00.0%
Mapped to wrong chromosome65241.561%
Mapped to wrong position104562.502%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.979200
Precision0.959400
Recall0.999900
Timing
Raw Mapping Time45.068s
Effective Mapping Time44.896s
Effective Init Time0.172s
Effective Time MeasureCPU
Mapping Time (Wall)19.095s
Mapping Time (CPU)45.068s
Mapping Time (CPU User)43.064s
Mapping Time (CPU System)2.004s
Init Time (Wall)0.213s
Init Time (CPU)0.172s
Init Time (CPU User)0.004s
Init Time (CPU System)0.168s
Additional Information
Mapper Memory Usage455 MB
Total Test Runtime (Wall)68.327s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/C_elegans.fa 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/C_elegans.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq -t 4 > out_bwamem.sam
memory174556000
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 0.000 CPU sec, 0.001 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq
[main] Real time: 0.223 sec; CPU: 0.156 sec
systime0.168
time0.244715929031
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq -t 4 > out_bwamem.sam
memory174552000
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 0.000 CPU sec, 0.001 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq
[main] Real time: 0.187 sec; CPU: 0.156 sec
systime0.168
time0.212705850601
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/C_elegans.fa reads.fastq -t 4 > out_bwamem.sam
memory455508000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 417860 sequences (25071600 bp)...
[M::mem_process_seqs] Processed 417860 reads in 44.216 CPU sec, 11.192 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/C_elegans.fa reads.fastq
[main] Real time: 19.049 sec; CPU: 45.032 sec
systime2.004
time19.0952289104
usrtime43.064
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6