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 Mapped69047588.038%
Wrongly Mapped593417.566%
Not Mapped344744.396%
Total784290100.0%
Read Failure Statistics
Not mapped344744.396%
Missing in mapper output00.0%
Mapped to wrong chromosome458695.848%
Mapped to wrong position134721.718%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936400
Precision0.920900
Recall0.952400
Timing
Raw Mapping Time182.616s
Effective Mapping Time177.732s
Effective Init Time4.884s
Effective Time MeasureCPU
Mapping Time (Wall)70.754s
Mapping Time (CPU)182.616s
Mapping Time (CPU User)167.688s
Mapping Time (CPU System)14.928s
Init Time (Wall)5.438s
Init Time (CPU)4.884s
Init Time (CPU User)0.116s
Init Time (CPU System)4.768s
Additional Information
Mapper Memory Usage5905 MB
Total Test Runtime (Wall)175.875s
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
memory5365028000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 5.163 sec; CPU: 4.800 sec
systime4.692
time5.37367200851
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory5366540000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 5.297 sec; CPU: 4.872 sec
systime4.768
time5.43832206726
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory5905788000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 784290 sequences/pairs (31371600 bp) ...
[bsw2_stat] infer the insert size distribution from 51216 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (76, 98, 120)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (40, 208)
[bsw2_stat] mean and std.dev: (99.22, 31.08)
[bsw2_stat] low and high boundaries for proper pairs: (40, 252)
[bsw2_pair] #fixed=2971, #rescued=22162, #moved=3944
[bsw2_stat] infer the insert size distribution from 51299 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (76, 98, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (40, 211)
[bsw2_stat] mean and std.dev: (99.40, 31.26)
[bsw2_stat] low and high boundaries for proper pairs: (40, 256)
[bsw2_pair] #fixed=2892, #rescued=22272, #moved=4024
[bsw2_stat] infer the insert size distribution from 51555 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (76, 98, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (40, 211)
[bsw2_stat] mean and std.dev: (99.27, 31.23)
[bsw2_stat] low and high boundaries for proper pairs: (40, 256)
[bsw2_pair] #fixed=2848, #rescued=21887, #moved=4005
[bsw2_stat] infer the insert size distribution from 51608 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (76, 98, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (40, 211)
[bsw2_stat] mean and std.dev: (99.47, 31.13)
[bsw2_stat] low and high boundaries for proper pairs: (40, 256)
[bsw2_pair] #fixed=2839, #rescued=21959, #moved=4001
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 70.527 sec; CPU: 182.604 sec
systime14.928
time70.7535641193
usrtime167.688
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa