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 Mapped40289596.32%
Wrongly Mapped152463.645%
Not Mapped1470.035%
Total418288100.0%
Read Failure Statistics
Not mapped1440.034%
Missing in mapper output30.001%
Mapped to wrong chromosome96042.296%
Mapped to wrong position56421.349%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment60
Secondary Alignments0
F-Measure0.981300
Precision0.963500
Recall0.999600
Timing
Raw Mapping Time484.252s
Effective Mapping Time389.688s
Effective Init Time94.564s
Effective Time MeasureCPU
Mapping Time (Wall)259.559s
Mapping Time (CPU)484.252s
Mapping Time (CPU User)328.524s
Mapping Time (CPU System)155.728s
Init Time (Wall)95.640s
Init Time (CPU)94.564s
Init Time (CPU User)0.028s
Init Time (CPU System)94.536s
Additional Information
Mapper Memory Usage5693 MB
Total Test Runtime (Wall)506.206s
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
memory5365020000
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: 97.959 sec; CPU: 96.904 sec
systime96.908
time97.9825000763
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

/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
memory5365132000
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: 95.582 sec; CPU: 94.552 sec
systime94.536
time95.6401920319
usrtime0.028
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

/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
memory5693896000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 418288 sequences/pairs (31371600 bp) ...
[bsw2_stat] infer the insert size distribution from 41780 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (405, 449, 493)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (229, 669)
[bsw2_stat] mean and std.dev: (449.06, 65.35)
[bsw2_stat] low and high boundaries for proper pairs: (141, 757)
[bsw2_pair] #fixed=5909, #rescued=1150, #moved=549
[bsw2_stat] infer the insert size distribution from 41733 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (404, 448, 493)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (226, 671)
[bsw2_stat] mean and std.dev: (448.29, 65.44)
[bsw2_stat] low and high boundaries for proper pairs: (137, 760)
[bsw2_pair] #fixed=5861, #rescued=1210, #moved=581
[bsw2_stat] infer the insert size distribution from 41946 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (404, 449, 493)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (226, 671)
[bsw2_stat] mean and std.dev: (448.93, 65.70)
[bsw2_stat] low and high boundaries for proper pairs: (137, 760)
[bsw2_pair] #fixed=5948, #rescued=1158, #moved=550
[bsw2_stat] infer the insert size distribution from 41820 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (405, 449, 493)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (229, 669)
[bsw2_stat] mean and std.dev: (449.01, 65.71)
[bsw2_stat] low and high boundaries for proper pairs: (141, 757)
[bsw2_pair] #fixed=5918, #rescued=1109, #moved=558
[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: 259.498 sec; CPU: 484.212 sec
systime155.728
time259.558516026
usrtime328.524
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1