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 Mapped30280296.522%
Wrongly Mapped106913.408%
Not Mapped2190.07%
Total313712100.0%
Read Failure Statistics
Not mapped1100.035%
Missing in mapper output1090.035%
Mapped to wrong chromosome68012.168%
Mapped to wrong position38901.24%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment265
Secondary Alignments0
F-Measure0.982500
Precision0.965900
Recall0.999600
Timing
Raw Mapping Time44.974s
Effective Mapping Time9.494s
Effective Init Time35.480s
Effective Time MeasureWall clock
Mapping Time (Wall)44.974s
Mapping Time (CPU)158.584s
Mapping Time (CPU User)155.404s
Mapping Time (CPU System)3.180s
Init Time (Wall)35.480s
Init Time (CPU)5.359s
Init Time (CPU User)0.053s
Init Time (CPU System)5.306s
Additional Information
Mapper Memory Usage5715 MB
Total Test Runtime (Wall)150.093s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5363560000
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: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq

[main] Real time: 58.715 sec; CPU: 7.629 sec
systime7.598844
time58.8109850883
usrtime0.032994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5363556000
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: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads_base.fastq

[main] Real time: 35.427 sec; CPU: 5.356 sec
systime5.306193
time35.480080843
usrtime0.052991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory5715712000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 313716 sequences/pairs (31371600 bp) ...

[bsw2_stat] infer the insert size distribution from 32289 high-quality pairs.

[bsw2_stat] (25, 50, 75) percentile: (466, 500, 533)

[bsw2_stat] low and high boundaries for computing mean and std.dev: (332, 667)

[bsw2_stat] mean and std.dev: (499.56, 49.90)

[bsw2_stat] low and high boundaries for proper pairs: (265, 734)

[bsw2_pair] #fixed=938, #rescued=1023, #moved=186

[bsw2_stat] infer the insert size distribution from 32329 high-quality pairs.

[bsw2_stat] (25, 50, 75) percentile: (467, 500, 534)

[bsw2_stat] low and high boundaries for computing mean and std.dev: (333, 668)

[bsw2_stat] mean and std.dev: (500.53, 49.77)

[bsw2_stat] low and high boundaries for proper pairs: (266, 735)

[bsw2_pair] #fixed=967, #rescued=1000, #moved=218

[bsw2_stat] infer the insert size distribution from 32269 high-quality pairs.

[bsw2_stat] (25, 50, 75) percentile: (466, 500, 534)

[bsw2_stat] low and high boundaries for computing mean and std.dev: (330, 670)

[bsw2_stat] mean and std.dev: (500.00, 50.04)

[bsw2_stat] low and high boundaries for proper pairs: (262, 738)

[bsw2_pair] #fixed=951, #rescued=1029, #moved=237

[bsw2_stat] infer the insert size distribution from 32225 high-quality pairs.

[bsw2_stat] (25, 50, 75) percentile: (466, 500, 534)

[bsw2_stat] low and high boundaries for computing mean and std.dev: (330, 670)

[bsw2_stat] mean and std.dev: (500.34, 49.83)

[bsw2_stat] low and high boundaries for proper pairs: (262, 738)

[bsw2_pair] #fixed=944, #rescued=1064, #moved=225

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/GRCh37.fa reads1.fastq reads2.fastq

[main] Real time: 44.957 sec; CPU: 158.576 sec
systime3.179516
time44.9738528728
usrtime155.404374
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H1_n