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 Mapped32428091.152%
Wrongly Mapped314768.848%
Not Mapped00.0%
Total355756100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome169434.763%
Mapped to wrong position145334.085%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953700
Precision0.911500
Recall1.000000
Timing
Raw Mapping Time84.772s
Effective Mapping Time84.528s
Effective Init Time0.244s
Effective Time MeasureCPU
Mapping Time (Wall)31.964s
Mapping Time (CPU)84.772s
Mapping Time (CPU User)82.532s
Mapping Time (CPU System)2.240s
Init Time (Wall)0.303s
Init Time (CPU)0.244s
Init Time (CPU User)0.032s
Init Time (CPU System)0.212s
Additional Information
Mapper Memory Usage611 MB
Total Test Runtime (Wall)84.201s
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
memory250620000
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, 0.003 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: 0.269 sec; CPU: 0.232 sec
systime0.224
time0.292038917542
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/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, 0.003 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: 0.276 sec; CPU: 0.232 sec
systime0.212
time0.303277015686
usrtime0.032
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/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
memory611520000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 355756 sequences (35931356 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 147961, 169, 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: (77, 99, 121)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 209)
[M::mem_pestat] mean and std.dev: (99.11, 32.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 253)
[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 355756 reads in 82.988 CPU sec, 20.918 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: 31.920 sec; CPU: 84.760 sec
systime2.24
time31.9641640186
usrtime82.532
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517