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 Mapped49455194.586%
Wrongly Mapped267275.112%
Not Mapped15820.303%
Total522860100.0%
Read Failure Statistics
Not mapped15810.302%
Missing in mapper output10.0%
Mapped to wrong chromosome187333.583%
Mapped to wrong position79911.528%
Mapped to wrong strand30.001%
Advanced Statistics
Missing in comparison alignment47
Secondary Alignments0
F-Measure0.972200
Precision0.948700
Recall0.996800
Timing
Raw Mapping Time268.668s
Effective Mapping Time264.296s
Effective Init Time4.372s
Effective Time MeasureCPU
Mapping Time (Wall)115.363s
Mapping Time (CPU)268.668s
Mapping Time (CPU User)251.144s
Mapping Time (CPU System)17.524s
Init Time (Wall)4.437s
Init Time (CPU)4.372s
Init Time (CPU User)0.084s
Init Time (CPU System)4.288s
Additional Information
Mapper Memory Usage5752 MB
Total Test Runtime (Wall)186.574s
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
memory5365028000
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: 4.415 sec; CPU: 4.356 sec
systime4.264
time4.43680810928
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/24f21f076cb23e5eaf20f9023e376370

/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
memory5366684000
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: 4.409 sec; CPU: 4.360 sec
systime4.288
time4.43738818169
usrtime0.084
working_directory/project/teaser/genometeaser/tests_generated/24f21f076cb23e5eaf20f9023e376370

/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
memory5752884000
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 49401 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: (102.48, 27.64)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=5040, #rescued=4526, #moved=614
[bsw2_stat] infer the insert size distribution from 49270 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: (102.53, 27.72)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4809, #rescued=4619, #moved=549
[bsw2_stat] infer the insert size distribution from 49555 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, 27.64)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4864, #rescued=4519, #moved=550
[bsw2_stat] infer the insert size distribution from 49367 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: (102.35, 27.56)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4972, #rescued=4586, #moved=560
[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: 115.322 sec; CPU: 268.660 sec
systime17.524
time115.363496065
usrtime251.144
working_directory/project/teaser/genometeaser/tests_generated/24f21f076cb23e5eaf20f9023e376370