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 Mapped32435790.271%
Wrongly Mapped349559.728%
Not Mapped20.001%
Total359314100.0%
Read Failure Statistics
Not mapped20.001%
Missing in mapper output00.0%
Mapped to wrong chromosome199705.558%
Mapped to wrong position149854.17%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment27
Secondary Alignments0
F-Measure0.948900
Precision0.902700
Recall1.000000
Timing
Raw Mapping Time285.198s
Effective Mapping Time285.064s
Effective Init Time0.134s
Effective Time MeasureCPU
Mapping Time (Wall)150.865s
Mapping Time (CPU)285.198s
Mapping Time (CPU User)283.941s
Mapping Time (CPU System)1.257s
Init Time (Wall)0.170s
Init Time (CPU)0.134s
Init Time (CPU User)0.006s
Init Time (CPU System)0.128s
Additional Information
Mapper Memory Usage524 MB
Total Test Runtime (Wall)168.245s
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
memory247276000
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: 0.307 sec; CPU: 0.156 sec
systime0.148977
time0.310463905334
usrtime0.009998
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

/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
memory247276000
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: 0.166 sec; CPU: 0.131 sec
systime0.12798
time0.169857978821
usrtime0.005999
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

/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
memory524948000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 359314 sequences/pairs (35931400 bp) ...
[bsw2_stat] infer the insert size distribution from 37214 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 122, 137)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 191)
[bsw2_stat] mean and std.dev: (125.39, 18.86)
[bsw2_stat] low and high boundaries for proper pairs: (100, 218)
[bsw2_pair] #fixed=4017, #rescued=45, #moved=18
[bsw2_stat] infer the insert size distribution from 37160 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 122, 137)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 191)
[bsw2_stat] mean and std.dev: (125.39, 18.84)
[bsw2_stat] low and high boundaries for proper pairs: (100, 218)
[bsw2_pair] #fixed=4003, #rescued=57, #moved=19
[bsw2_stat] infer the insert size distribution from 37277 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 122, 137)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 191)
[bsw2_stat] mean and std.dev: (125.55, 18.86)
[bsw2_stat] low and high boundaries for proper pairs: (100, 218)
[bsw2_pair] #fixed=4115, #rescued=49, #moved=17
[bsw2_stat] infer the insert size distribution from 37212 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 122, 137)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 191)
[bsw2_stat] mean and std.dev: (125.40, 18.98)
[bsw2_stat] low and high boundaries for proper pairs: (100, 218)
[bsw2_pair] #fixed=4012, #rescued=64, #moved=20
[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: 150.851 sec; CPU: 285.186 sec
systime1.256808
time150.865350008
usrtime283.940834
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e