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 Mapped22246596.402%
Wrongly Mapped82653.582%
Not Mapped380.016%
Total230768100.0%
Read Failure Statistics
Not mapped380.016%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position82653.582%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment14
Secondary Alignments0
F-Measure0.981700
Precision0.964200
Recall0.999800
Timing
Raw Mapping Time168.912s
Effective Mapping Time168.852s
Effective Init Time0.060s
Effective Time MeasureCPU
Mapping Time (Wall)64.022s
Mapping Time (CPU)168.912s
Mapping Time (CPU User)161.980s
Mapping Time (CPU System)6.932s
Init Time (Wall)0.133s
Init Time (CPU)0.060s
Init Time (CPU User)0.004s
Init Time (CPU System)0.056s
Additional Information
Mapper Memory Usage184 MB
Total Test Runtime (Wall)96.116s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.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/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory16084000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.112 sec; CPU: 0.044 sec
systime0.04
time0.140562057495
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory16084000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.096 sec; CPU: 0.048 sec
systime0.056
time0.132982969284
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory184564000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 230768 sequences/pairs (14999920 bp) ...
[bsw2_stat] infer the insert size distribution from 26505 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (127, 149, 171)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (65, 259)
[bsw2_stat] mean and std.dev: (149.24, 32.39)
[bsw2_stat] low and high boundaries for proper pairs: (65, 303)
[bsw2_pair] #fixed=2605, #rescued=611, #moved=86
[bsw2_stat] infer the insert size distribution from 26485 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (127, 150, 172)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (65, 262)
[bsw2_stat] mean and std.dev: (149.55, 32.58)
[bsw2_stat] low and high boundaries for proper pairs: (65, 307)
[bsw2_pair] #fixed=2609, #rescued=632, #moved=88
[bsw2_stat] infer the insert size distribution from 26441 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (126, 149, 171)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (65, 261)
[bsw2_stat] mean and std.dev: (148.87, 32.67)
[bsw2_stat] low and high boundaries for proper pairs: (65, 306)
[bsw2_pair] #fixed=2606, #rescued=632, #moved=75
[bsw2_stat] infer the insert size distribution from 26436 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (127, 149, 171)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (65, 259)
[bsw2_stat] mean and std.dev: (149.20, 32.60)
[bsw2_stat] low and high boundaries for proper pairs: (65, 303)
[bsw2_pair] #fixed=2627, #rescued=671, #moved=88
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads1.fastq reads2.fastq
[main] Real time: 63.965 sec; CPU: 168.904 sec
systime6.932
time64.021655798
usrtime161.98
working_directory/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80