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 Mapped9909399.093%
Wrongly Mapped9070.907%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome6830.683%
Mapped to wrong position2240.224%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.995400
Precision0.990900
Recall1.000000
Timing
Raw Mapping Time91.220s
Effective Mapping Time91.172s
Effective Init Time0.048s
Effective Time MeasureCPU
Mapping Time (Wall)43.654s
Mapping Time (CPU)91.220s
Mapping Time (CPU User)89.256s
Mapping Time (CPU System)1.964s
Init Time (Wall)0.117s
Init Time (CPU)0.048s
Init Time (CPU User)0.012s
Init Time (CPU System)0.036s
Additional Information
Mapper Memory Usage144 MB
Total Test Runtime (Wall)63.874s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.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/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory24540000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.062 sec; CPU: 0.036 sec
systime0.036
time0.0821979045868
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory25852000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.072 sec; CPU: 0.040 sec
systime0.036
time0.116539001465
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory144944000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 100000 sequences/pairs (15000000 bp) ...
[bsw2_stat] infer the insert size distribution from 12054 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (376, 399, 421)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (286, 511)
[bsw2_stat] mean and std.dev: (399.02, 33.18)
[bsw2_stat] low and high boundaries for proper pairs: (241, 556)
[bsw2_pair] #fixed=2501, #rescued=23, #moved=6
[bsw2_stat] infer the insert size distribution from 12078 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 399, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (287, 512)
[bsw2_stat] mean and std.dev: (399.52, 33.44)
[bsw2_stat] low and high boundaries for proper pairs: (242, 557)
[bsw2_pair] #fixed=2642, #rescued=11, #moved=13
[bsw2_stat] infer the insert size distribution from 12073 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (376, 400, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (284, 514)
[bsw2_stat] mean and std.dev: (399.23, 33.48)
[bsw2_stat] low and high boundaries for proper pairs: (238, 560)
[bsw2_pair] #fixed=2599, #rescued=21, #moved=9
[bsw2_stat] infer the insert size distribution from 12053 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (376, 399, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (284, 514)
[bsw2_stat] mean and std.dev: (399.20, 33.69)
[bsw2_stat] low and high boundaries for proper pairs: (238, 560)
[bsw2_pair] #fixed=2635, #rescued=18, #moved=5
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq
[main] Real time: 43.626 sec; CPU: 91.204 sec
systime1.964
time43.6544780731
usrtime89.256
working_directory/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05