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 Mapped49403594.487%
Wrongly Mapped271885.2%
Not Mapped16370.313%
Total522860100.0%
Read Failure Statistics
Not mapped16360.313%
Missing in mapper output10.0%
Mapped to wrong chromosome192353.679%
Mapped to wrong position79521.521%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment44
Secondary Alignments0
F-Measure0.971700
Precision0.947800
Recall0.996700
Timing
Raw Mapping Time263.964s
Effective Mapping Time259.564s
Effective Init Time4.400s
Effective Time MeasureCPU
Mapping Time (Wall)120.068s
Mapping Time (CPU)263.964s
Mapping Time (CPU User)248.496s
Mapping Time (CPU System)15.468s
Init Time (Wall)4.480s
Init Time (CPU)4.400s
Init Time (CPU User)0.104s
Init Time (CPU System)4.296s
Additional Information
Mapper Memory Usage5752 MB
Total Test Runtime (Wall)190.843s
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
memory5366548000
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: 4.451 sec; CPU: 4.392 sec
systime4.308
time4.47393989563
usrtime0.096
working_directory/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e

/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: 4.448 sec; CPU: 4.392 sec
systime4.296
time4.47978377342
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e

/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
memory5752856000
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 49236 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, 27.57)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4888, #rescued=4549, #moved=598
[bsw2_stat] infer the insert size distribution from 49211 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: (102.53, 27.63)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=5000, #rescued=4646, #moved=533
[bsw2_stat] infer the insert size distribution from 49332 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: (102.38, 27.51)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=4999, #rescued=4554, #moved=592
[bsw2_stat] infer the insert size distribution from 49379 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: (102.46, 27.63)
[bsw2_stat] low and high boundaries for proper pairs: (60, 244)
[bsw2_pair] #fixed=5075, #rescued=4455, #moved=581
[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: 120.023 sec; CPU: 263.952 sec
systime15.468
time120.068359137
usrtime248.496
working_directory/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e