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 Mapped50394296.382%
Wrongly Mapped189183.618%
Not Mapped00.0%
Total522860100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome125212.395%
Mapped to wrong position63971.223%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.981600
Precision0.963800
Recall1.000000
Timing
Raw Mapping Time197.396s
Effective Mapping Time192.660s
Effective Init Time4.736s
Effective Time MeasureCPU
Mapping Time (Wall)64.984s
Mapping Time (CPU)197.396s
Mapping Time (CPU User)186.716s
Mapping Time (CPU System)10.680s
Init Time (Wall)4.811s
Init Time (CPU)4.736s
Init Time (CPU User)0.084s
Init Time (CPU System)4.652s
Additional Information
Mapper Memory Usage6214 MB
Total Test Runtime (Wall)139.736s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.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/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5365832000
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 0.008 CPU sec, 0.003 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 6.198 sec; CPU: 6.136 sec
systime6.032
time6.26955795288
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwamem.sam
memory5365896000
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 0.004 CPU sec, 0.003 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.779 sec; CPU: 4.724 sec
systime4.652
time4.81131196022
usrtime0.084
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory6214828000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 522860 sequences (31371600 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 210551, 272, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (76, 98, 120)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 208)
[M::mem_pestat] mean and std.dev: (98.04, 32.43)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 252)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1, 1, 1)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1)
[M::mem_pestat] mean and std.dev: (1.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 522860 reads in 190.008 CPU sec, 47.975 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 64.942 sec; CPU: 197.368 sec
systime10.68
time64.9839320183
usrtime186.716
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6