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 Mapped74601195.119%
Wrongly Mapped381784.868%
Not Mapped1010.013%
Total784290100.0%
Read Failure Statistics
Not mapped1010.013%
Missing in mapper output00.0%
Mapped to wrong chromosome263023.354%
Mapped to wrong position118761.514%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.975000
Precision0.951300
Recall0.999900
Timing
Raw Mapping Time325.436s
Effective Mapping Time320.124s
Effective Init Time5.312s
Effective Time MeasureCPU
Mapping Time (Wall)100.842s
Mapping Time (CPU)325.436s
Mapping Time (CPU User)309.392s
Mapping Time (CPU System)16.044s
Init Time (Wall)5.620s
Init Time (CPU)5.312s
Init Time (CPU User)0.192s
Init Time (CPU System)5.120s
Additional Information
Mapper Memory Usage7105 MB
Total Test Runtime (Wall)216.510s
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
memory5364624000
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, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 5.453 sec; CPU: 5.284 sec
systime5.204
time5.4860830307
usrtime0.092
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory5365828000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 5.531 sec; CPU: 5.300 sec
systime5.12
time5.61984992027
usrtime0.192
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory7105440000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 784290 sequences (31371600 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 282730, 381, 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: (97.74, 32.66)
[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 784290 reads in 318.768 CPU sec, 81.074 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 100.722 sec; CPU: 325.428 sec
systime16.044
time100.842211008
usrtime309.392
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa