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 Mapped53460489.271%
Wrongly Mapped6327310.566%
Not Mapped9810.164%
Total598858100.0%
Read Failure Statistics
Not mapped9790.163%
Missing in mapper output20.0%
Mapped to wrong chromosome372496.22%
Mapped to wrong position260244.346%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment22
Secondary Alignments0
F-Measure0.943300
Precision0.894200
Recall0.998200
Timing
Raw Mapping Time433.104s
Effective Mapping Time431.656s
Effective Init Time1.448s
Effective Time MeasureCPU
Mapping Time (Wall)123.426s
Mapping Time (CPU)433.104s
Mapping Time (CPU User)418.128s
Mapping Time (CPU System)14.976s
Init Time (Wall)1.528s
Init Time (CPU)1.448s
Init Time (CPU User)0.016s
Init Time (CPU System)1.432s
Additional Information
Mapper Memory Usage686 MB
Total Test Runtime (Wall)206.990s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248996000
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: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 1.703 sec; CPU: 1.652 sec
systime1.652
time1.72634410858
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248992000
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: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 1.500 sec; CPU: 1.436 sec
systime1.432
time1.52767586708
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory686452000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 598858 sequences/pairs (35931480 bp) ...
[bsw2_stat] infer the insert size distribution from 58820 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 100, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.83, 27.69)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=6982, #rescued=3652, #moved=404
[bsw2_stat] infer the insert size distribution from 58870 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 100, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.93, 27.77)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=7131, #rescued=3599, #moved=359
[bsw2_stat] infer the insert size distribution from 58843 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (80, 100, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 203)
[bsw2_stat] mean and std.dev: (102.89, 27.74)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=7063, #rescued=3661, #moved=416
[bsw2_stat] infer the insert size distribution from 58953 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: (102.68, 27.70)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=7020, #rescued=3624, #moved=413
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 123.368 sec; CPU: 433.064 sec
systime14.976
time123.425709963
usrtime418.128
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380