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 Mapped57333993.206%
Wrongly Mapped360235.856%
Not Mapped57660.937%
Total615128100.0%
Read Failure Statistics
Not mapped57660.937%
Missing in mapper output00.0%
Mapped to wrong chromosome269984.389%
Mapped to wrong position90251.467%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment15
Secondary Alignments0
F-Measure0.964800
Precision0.940900
Recall0.990000
Timing
Raw Mapping Time364.168s
Effective Mapping Time337.304s
Effective Init Time26.864s
Effective Time MeasureCPU
Mapping Time (Wall)191.925s
Mapping Time (CPU)364.168s
Mapping Time (CPU User)312.280s
Mapping Time (CPU System)51.888s
Init Time (Wall)29.302s
Init Time (CPU)26.864s
Init Time (CPU User)0.244s
Init Time (CPU System)26.620s
Additional Information
Mapper Memory Usage5795 MB
Total Test Runtime (Wall)338.408s
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
memory5364912000
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: 36.982 sec; CPU: 33.968 sec
systime33.592
time37.0238189697
usrtime0.388
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/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
memory5364904000
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: 29.240 sec; CPU: 26.840 sec
systime26.62
time29.3015010357
usrtime0.244
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d

/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
memory5795924000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 615128 sequences/pairs (31371528 bp) ...
[bsw2_stat] infer the insert size distribution from 51963 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (77, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (51, 209)
[bsw2_stat] mean and std.dev: (100.69, 29.63)
[bsw2_stat] low and high boundaries for proper pairs: (51, 253)
[bsw2_pair] #fixed=4800, #rescued=9789, #moved=1286
[bsw2_stat] infer the insert size distribution from 51824 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (77, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (51, 209)
[bsw2_stat] mean and std.dev: (100.99, 29.68)
[bsw2_stat] low and high boundaries for proper pairs: (51, 253)
[bsw2_pair] #fixed=4634, #rescued=9949, #moved=1255
[bsw2_stat] infer the insert size distribution from 51827 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (78, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (51, 207)
[bsw2_stat] mean and std.dev: (100.92, 29.49)
[bsw2_stat] low and high boundaries for proper pairs: (51, 250)
[bsw2_pair] #fixed=4768, #rescued=9865, #moved=1340
[bsw2_stat] infer the insert size distribution from 51778 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (77, 99, 121)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (51, 209)
[bsw2_stat] mean and std.dev: (100.83, 29.65)
[bsw2_stat] low and high boundaries for proper pairs: (51, 253)
[bsw2_pair] #fixed=4686, #rescued=9820, #moved=1371
[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: 191.789 sec; CPU: 364.124 sec
systime51.888
time191.925414085
usrtime312.28
working_directory/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d