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 Mapped29463593.919%
Wrongly Mapped144874.618%
Not Mapped45911.463%
Total313713100.0%
Read Failure Statistics
Not mapped44591.421%
Missing in mapper output1320.042%
Mapped to wrong chromosome105693.369%
Mapped to wrong position39181.249%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment274
Secondary Alignments0
F-Measure0.968800
Precision0.953100
Recall0.985100
Timing
Raw Mapping Time40.998s
Effective Mapping Time39.925s
Effective Init Time1.073s
Effective Time MeasureWall clock
Mapping Time (Wall)40.998s
Mapping Time (CPU)149.589s
Mapping Time (CPU User)147.198s
Mapping Time (CPU System)2.392s
Init Time (Wall)1.073s
Init Time (CPU)1.064s
Init Time (CPU User)0.020s
Init Time (CPU System)1.044s
Additional Information
Mapper Memory Usage5715 MB
Total Test Runtime (Wall)54.610s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5363556000
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: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq

[main] Real time: 1.078 sec; CPU: 1.073 sec
systime1.04884
time1.08621501923
usrtime0.026995
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5363560000
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: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq

[main] Real time: 1.064 sec; CPU: 1.061 sec
systime1.043841
time1.07281112671
usrtime0.019996
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads.fastq -t 4 > out_bwasw.sam
memory5715500000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 313716 sequences/pairs (31371600 bp) ...

[main] Version: 0.7.12-r1039

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

[main] Real time: 40.985 sec; CPU: 149.579 sec
systime2.391636
time40.9976642132
usrtime147.197622
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n