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 Mapped22144092.443%
Wrongly Mapped181027.557%
Not Mapped00.0%
Total239542100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome94873.96%
Mapped to wrong position86153.596%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.960700
Precision0.924400
Recall1.000000
Timing
Raw Mapping Time99.897s
Effective Mapping Time99.721s
Effective Init Time0.176s
Effective Time MeasureCPU
Mapping Time (Wall)34.822s
Mapping Time (CPU)99.897s
Mapping Time (CPU User)99.480s
Mapping Time (CPU System)0.417s
Init Time (Wall)0.318s
Init Time (CPU)0.176s
Init Time (CPU User)0.009s
Init Time (CPU System)0.167s
Additional Information
Mapper Memory Usage494 MB
Total Test Runtime (Wall)50.888s
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
memory247132000
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 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.185 sec; CPU: 0.141 sec
systime0.135979
time0.191612005234
usrtime0.009998
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/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
memory247132000
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 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.199 sec; CPU: 0.172 sec
systime0.166974
time0.318073987961
usrtime0.008998
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/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
memory494060000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 239542 sequences (35931300 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 100084, 109, 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: (79, 101, 123)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 211)
[M::mem_pestat] mean and std.dev: (100.78, 32.51)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 255)
[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 239542 reads in 99.417 CPU sec, 33.258 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 34.810 sec; CPU: 99.886 sec
systime0.416936
time34.822053194
usrtime99.479876
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae