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 Mapped74331085.298%
Wrongly Mapped618947.103%
Not Mapped662287.6%
Total871432100.0%
Read Failure Statistics
Not mapped662287.6%
Missing in mapper output00.0%
Mapped to wrong chromosome481825.529%
Mapped to wrong position137101.573%
Mapped to wrong strand20.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.920700
Precision0.923100
Recall0.918200
Timing
Raw Mapping Time198.968s
Effective Mapping Time194.380s
Effective Init Time4.588s
Effective Time MeasureCPU
Mapping Time (Wall)78.566s
Mapping Time (CPU)198.968s
Mapping Time (CPU User)179.668s
Mapping Time (CPU System)19.300s
Init Time (Wall)4.659s
Init Time (CPU)4.588s
Init Time (CPU User)0.092s
Init Time (CPU System)4.496s
Additional Information
Mapper Memory Usage5930 MB
Total Test Runtime (Wall)182.305s
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: 4.618 sec; CPU: 4.560 sec
systime4.484
time4.64035010338
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/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
memory5366680000
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: 4.628 sec; CPU: 4.580 sec
systime4.496
time4.65865302086
usrtime0.092
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/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
memory5930580000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 871432 sequences/pairs (31371552 bp) ...
[bsw2_stat] infer the insert size distribution from 55357 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 199, 221)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (89, 309)
[bsw2_stat] mean and std.dev: (198.87, 32.86)
[bsw2_stat] low and high boundaries for proper pairs: (45, 353)
[bsw2_pair] #fixed=6435, #rescued=16823, #moved=4112
[bsw2_stat] infer the insert size distribution from 55159 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 199, 221)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (89, 309)
[bsw2_stat] mean and std.dev: (199.11, 32.78)
[bsw2_stat] low and high boundaries for proper pairs: (45, 353)
[bsw2_pair] #fixed=6451, #rescued=16926, #moved=4145
[bsw2_stat] infer the insert size distribution from 55290 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 199, 221)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (89, 309)
[bsw2_stat] mean and std.dev: (199.11, 32.65)
[bsw2_stat] low and high boundaries for proper pairs: (45, 353)
[bsw2_pair] #fixed=6561, #rescued=16814, #moved=4137
[bsw2_stat] infer the insert size distribution from 55477 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (177, 199, 221)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (89, 309)
[bsw2_stat] mean and std.dev: (199.08, 32.78)
[bsw2_stat] low and high boundaries for proper pairs: (45, 353)
[bsw2_pair] #fixed=6478, #rescued=16853, #moved=4168
[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: 78.507 sec; CPU: 198.960 sec
systime19.3
time78.5661900043
usrtime179.668
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf