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 Mapped16429492.363%
Wrongly Mapped135837.636%
Not Mapped10.001%
Total177878100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output10.001%
Mapped to wrong chromosome71093.997%
Mapped to wrong position64743.64%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment9
Secondary Alignments0
F-Measure0.960300
Precision0.923600
Recall1.000000
Timing
Raw Mapping Time370.756s
Effective Mapping Time368.884s
Effective Init Time1.872s
Effective Time MeasureCPU
Mapping Time (Wall)118.003s
Mapping Time (CPU)370.756s
Mapping Time (CPU User)363.720s
Mapping Time (CPU System)7.036s
Init Time (Wall)1.994s
Init Time (CPU)1.872s
Init Time (CPU User)0.012s
Init Time (CPU System)1.860s
Additional Information
Mapper Memory Usage491 MB
Total Test Runtime (Wall)158.518s
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
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: 2.237 sec; CPU: 2.160 sec
systime2.148
time2.25807285309
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/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: 1.938 sec; CPU: 1.856 sec
systime1.86
time1.99403500557
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/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
memory491924000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 177878 sequences/pairs (35931356 bp) ...
[bsw2_stat] infer the insert size distribution from 18620 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (279, 302, 324)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (202, 414)
[bsw2_stat] mean and std.dev: (301.51, 32.95)
[bsw2_stat] low and high boundaries for proper pairs: (202, 459)
[bsw2_pair] #fixed=18, #rescued=0, #moved=4
[bsw2_stat] infer the insert size distribution from 18452 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (279, 302, 324)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (202, 414)
[bsw2_stat] mean and std.dev: (301.63, 33.01)
[bsw2_stat] low and high boundaries for proper pairs: (202, 459)
[bsw2_pair] #fixed=14, #rescued=0, #moved=3
[bsw2_stat] infer the insert size distribution from 18480 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (279, 302, 324)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (202, 414)
[bsw2_stat] mean and std.dev: (301.80, 33.08)
[bsw2_stat] low and high boundaries for proper pairs: (202, 459)
[bsw2_pair] #fixed=15, #rescued=0, #moved=2
[bsw2_stat] infer the insert size distribution from 18563 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (280, 302, 324)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (202, 412)
[bsw2_stat] mean and std.dev: (301.88, 32.53)
[bsw2_stat] low and high boundaries for proper pairs: (202, 456)
[bsw2_pair] #fixed=13, #rescued=0, #moved=6
[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: 117.955 sec; CPU: 370.716 sec
systime7.036
time118.002507925
usrtime363.72
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f