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 Mapped9909099.09%
Wrongly Mapped9100.91%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome6710.671%
Mapped to wrong position2390.239%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment1
Secondary Alignments0
F-Measure0.995400
Precision0.990900
Recall1.000000
Timing
Raw Mapping Time90.320s
Effective Mapping Time90.268s
Effective Init Time0.052s
Effective Time MeasureCPU
Mapping Time (Wall)48.917s
Mapping Time (CPU)90.320s
Mapping Time (CPU User)88.260s
Mapping Time (CPU System)2.060s
Init Time (Wall)6.115s
Init Time (CPU)0.052s
Init Time (CPU User)0.020s
Init Time (CPU System)0.032s
Additional Information
Mapper Memory Usage143 MB
Total Test Runtime (Wall)101.888s
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
memory24616000
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: 4.990 sec; CPU: 0.044 sec
systime0.044
time5.88083291054
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3

/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
memory26180000
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: 4.989 sec; CPU: 0.044 sec
systime0.032
time6.11463880539
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3

/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
memory143920000
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 12047 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: (398.82, 32.98)
[bsw2_stat] low and high boundaries for proper pairs: (241, 556)
[bsw2_pair] #fixed=2643, #rescued=21, #moved=16
[bsw2_stat] infer the insert size distribution from 12058 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 400, 423)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (285, 515)
[bsw2_stat] mean and std.dev: (399.81, 33.92)
[bsw2_stat] low and high boundaries for proper pairs: (239, 561)
[bsw2_pair] #fixed=2584, #rescued=16, #moved=11
[bsw2_stat] infer the insert size distribution from 12054 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 399, 421)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (289, 509)
[bsw2_stat] mean and std.dev: (398.83, 33.28)
[bsw2_stat] low and high boundaries for proper pairs: (245, 553)
[bsw2_pair] #fixed=2605, #rescued=13, #moved=9
[bsw2_stat] infer the insert size distribution from 12104 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 400, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (287, 512)
[bsw2_stat] mean and std.dev: (399.61, 33.56)
[bsw2_stat] low and high boundaries for proper pairs: (242, 557)
[bsw2_pair] #fixed=2609, #rescued=13, #moved=6
[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: 48.195 sec; CPU: 90.312 sec
systime2.06
time48.9166929722
usrtime88.26
working_directory/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3