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 Mapped49335094.356%
Wrongly Mapped278575.328%
Not Mapped16530.316%
Total522860100.0%
Read Failure Statistics
Not mapped16510.316%
Missing in mapper output20.0%
Mapped to wrong chromosome197803.783%
Mapped to wrong position80771.545%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment42
Secondary Alignments0
F-Measure0.971000
Precision0.946600
Recall0.996700
Timing
Raw Mapping Time244.700s
Effective Mapping Time239.916s
Effective Init Time4.784s
Effective Time MeasureCPU
Mapping Time (Wall)101.159s
Mapping Time (CPU)244.700s
Mapping Time (CPU User)231.932s
Mapping Time (CPU System)12.768s
Init Time (Wall)4.873s
Init Time (CPU)4.784s
Init Time (CPU User)0.120s
Init Time (CPU System)4.664s
Additional Information
Mapper Memory Usage5752 MB
Total Test Runtime (Wall)173.020s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5364892000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.850 sec; CPU: 4.780 sec
systime4.668
time4.87167286873
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366552000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.838 sec; CPU: 4.776 sec
systime4.664
time4.87315797806
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory5752948000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 522860 sequences/pairs (31371600 bp) ...
[bsw2_stat] infer the insert size distribution from 49387 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.37, 27.53)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4934, #rescued=4448, #moved=553
[bsw2_stat] infer the insert size distribution from 49129 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.51, 27.72)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4911, #rescued=4501, #moved=575
[bsw2_stat] infer the insert size distribution from 49273 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.55, 27.60)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4878, #rescued=4583, #moved=548
[bsw2_stat] infer the insert size distribution from 49119 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.40, 27.54)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=5024, #rescued=4557, #moved=617
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 101.102 sec; CPU: 244.688 sec
systime12.768
time101.159147978
usrtime231.932
working_directory/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e