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 Mapped65044090.511%
Wrongly Mapped681889.489%
Not Mapped00.0%
Total718628100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome375545.226%
Mapped to wrong position306344.263%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.950200
Precision0.905100
Recall1.000000
Timing
Raw Mapping Time105.308s
Effective Mapping Time105.052s
Effective Init Time0.256s
Effective Time MeasureCPU
Mapping Time (Wall)39.881s
Mapping Time (CPU)105.308s
Mapping Time (CPU User)101.608s
Mapping Time (CPU System)3.700s
Init Time (Wall)0.315s
Init Time (CPU)0.256s
Init Time (CPU User)0.020s
Init Time (CPU System)0.236s
Additional Information
Mapper Memory Usage1016 MB
Total Test Runtime (Wall)123.097s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248788000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.004 CPU sec, 0.001 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.284 sec; CPU: 0.244 sec
systime0.24
time0.306578874588
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory250616000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.004 CPU sec, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.286 sec; CPU: 0.248 sec
systime0.236
time0.315201044083
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory1016592000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 718628 sequences (35931400 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 293944, 17, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (106, 128, 151)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (16, 241)
[M::mem_pestat] mean and std.dev: (128.30, 32.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 286)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1, 1, 1)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1)
[M::mem_pestat] mean and std.dev: (1.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 718628 reads in 103.852 CPU sec, 26.363 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 39.833 sec; CPU: 105.300 sec
systime3.7
time39.8808889389
usrtime101.608
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6