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 Mapped30188896.231%
Wrongly Mapped117833.756%
Not Mapped420.013%
Total313713100.0%
Read Failure Statistics
Not mapped420.013%
Missing in mapper output00.0%
Mapped to wrong chromosome79772.543%
Mapped to wrong position38061.213%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments59
F-Measure0.980800
Precision0.962400
Recall0.999900
Timing
Raw Mapping Time29.116s
Effective Mapping Time28.027s
Effective Init Time1.089s
Effective Time MeasureWall clock
Mapping Time (Wall)29.116s
Mapping Time (CPU)103.868s
Mapping Time (CPU User)102.455s
Mapping Time (CPU System)1.413s
Init Time (Wall)1.089s
Init Time (CPU)1.084s
Init Time (CPU User)0.035s
Init Time (CPU System)1.049s
Additional Information
Mapper Memory Usage5820 MB
Total Test Runtime (Wall)43.830s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5363100000
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 0.003 CPU sec, 0.002 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq

[main] Real time: 1.384 sec; CPU: 1.269 sec
systime1.242811
time1.39573788643
usrtime0.028995
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5366628000
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 0.018 CPU sec, 0.016 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq

[main] Real time: 1.084 sec; CPU: 1.080 sec
systime1.04884
time1.08932185173
usrtime0.034994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq -t 4 > out_bwamem.sam
memory5820812000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 313716 sequences (31371600 bp)...

[M::mem_process_seqs] Processed 313716 reads in 102.468 CPU sec, 25.738 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq

[main] Real time: 29.106 sec; CPU: 103.861 sec
systime1.412785
time29.116079092
usrtime102.455424
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n