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 Mapped53676389.631%
Wrongly Mapped6150710.271%
Not Mapped5880.098%
Total598858100.0%
Read Failure Statistics
Not mapped5880.098%
Missing in mapper output00.0%
Mapped to wrong chromosome351815.875%
Mapped to wrong position263264.396%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment29
Secondary Alignments0
F-Measure0.945300
Precision0.897200
Recall0.998900
Timing
Raw Mapping Time377.892s
Effective Mapping Time375.704s
Effective Init Time2.188s
Effective Time MeasureCPU
Mapping Time (Wall)126.309s
Mapping Time (CPU)377.892s
Mapping Time (CPU User)359.920s
Mapping Time (CPU System)17.972s
Init Time (Wall)2.276s
Init Time (CPU)2.188s
Init Time (CPU User)0.016s
Init Time (CPU System)2.172s
Additional Information
Mapper Memory Usage686 MB
Total Test Runtime (Wall)212.855s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248988000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 1.579 sec; CPU: 1.508 sec
systime1.5
time1.61159777641
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248992000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 2.246 sec; CPU: 2.180 sec
systime2.172
time2.27558612823
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory686656000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 598858 sequences/pairs (35931480 bp) ...
[bsw2_stat] infer the insert size distribution from 58666 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (127, 149, 172)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 262)
[bsw2_stat] mean and std.dev: (149.20, 32.98)
[bsw2_stat] low and high boundaries for proper pairs: (60, 307)
[bsw2_pair] #fixed=8030, #rescued=3700, #moved=815
[bsw2_stat] infer the insert size distribution from 58743 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (127, 149, 171)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 259)
[bsw2_stat] mean and std.dev: (149.12, 32.71)
[bsw2_stat] low and high boundaries for proper pairs: (60, 303)
[bsw2_pair] #fixed=7869, #rescued=3728, #moved=810
[bsw2_stat] infer the insert size distribution from 58711 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (127, 149, 171)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 259)
[bsw2_stat] mean and std.dev: (149.45, 32.66)
[bsw2_stat] low and high boundaries for proper pairs: (60, 303)
[bsw2_pair] #fixed=8011, #rescued=3688, #moved=826
[bsw2_stat] infer the insert size distribution from 58642 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (127, 149, 171)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (60, 259)
[bsw2_stat] mean and std.dev: (149.26, 32.80)
[bsw2_stat] low and high boundaries for proper pairs: (60, 303)
[bsw2_pair] #fixed=8099, #rescued=3669, #moved=795
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 126.254 sec; CPU: 377.848 sec
systime17.972
time126.308817148
usrtime359.92
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62