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 Mapped9844898.448%
Wrongly Mapped15521.552%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome8060.806%
Mapped to wrong position7460.746%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.992200
Precision0.984500
Recall1.000000
Timing
Raw Mapping Time24.380s
Effective Mapping Time22.836s
Effective Init Time1.544s
Effective Time MeasureCPU
Mapping Time (Wall)11.115s
Mapping Time (CPU)24.380s
Mapping Time (CPU User)21.608s
Mapping Time (CPU System)2.772s
Init Time (Wall)1.649s
Init Time (CPU)1.544s
Init Time (CPU User)0.108s
Init Time (CPU System)1.436s
Additional Information
Mapper Memory Usage1887 MB
Total Test Runtime (Wall)31.658s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Gallus_gallus.fa 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/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwamem.sam
memory1796740000
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/Gallus_gallus.fa reads_base.fastq
[main] Real time: 1.609 sec; CPU: 1.532 sec
systime1.444
time1.64978098869
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwamem.sam
memory1795036000
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 0.008 CPU sec, 0.010 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq
[main] Real time: 1.620 sec; CPU: 1.528 sec
systime1.436
time1.64915394783
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory1887332000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 100000 sequences (15000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 47424, 0, 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: (95, 99, 103)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (79, 119)
[M::mem_pestat] mean and std.dev: (99.01, 6.59)
[M::mem_pestat] low and high boundaries for proper pairs: (71, 127)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 100000 reads in 22.544 CPU sec, 5.724 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq reads2.fastq
[main] Real time: 11.079 sec; CPU: 24.356 sec
systime2.772
time11.1145689487
usrtime21.608
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a