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 Mapped49427894.534%
Wrongly Mapped268925.143%
Not Mapped16900.323%
Total522860100.0%
Read Failure Statistics
Not mapped16870.323%
Missing in mapper output30.001%
Mapped to wrong chromosome193193.695%
Mapped to wrong position75731.448%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment49
Secondary Alignments0
F-Measure0.971900
Precision0.948400
Recall0.996600
Timing
Raw Mapping Time216.672s
Effective Mapping Time211.616s
Effective Init Time5.056s
Effective Time MeasureCPU
Mapping Time (Wall)70.143s
Mapping Time (CPU)216.672s
Mapping Time (CPU User)205.460s
Mapping Time (CPU System)11.212s
Init Time (Wall)5.151s
Init Time (CPU)5.056s
Init Time (CPU User)0.104s
Init Time (CPU System)4.952s
Additional Information
Mapper Memory Usage5753 MB
Total Test Runtime (Wall)146.901s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa 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/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5365088000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 5.449 sec; CPU: 5.384 sec
systime5.312
time5.47130322456
usrtime0.084
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5365084000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 5.119 sec; CPU: 5.048 sec
systime4.952
time5.15052103996
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory5753172000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 522860 sequences/pairs (31371600 bp) ...
[bsw2_stat] infer the insert size distribution from 49333 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: (102.56, 27.66)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4945, #rescued=4503, #moved=564
[bsw2_stat] infer the insert size distribution from 49271 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: (102.25, 27.66)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=5074, #rescued=4552, #moved=551
[bsw2_stat] infer the insert size distribution from 49278 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: (102.55, 27.64)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4945, #rescued=4400, #moved=607
[bsw2_stat] infer the insert size distribution from 49058 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: (102.62, 27.65)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=5041, #rescued=4528, #moved=577
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 70.087 sec; CPU: 216.628 sec
systime11.212
time70.1434090137
usrtime205.46
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6