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 Mapped9825098.25%
Wrongly Mapped17501.75%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome9350.935%
Mapped to wrong position8150.815%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment1
Secondary Alignments0
F-Measure0.991200
Precision0.982500
Recall1.000000
Timing
Raw Mapping Time117.560s
Effective Mapping Time116.020s
Effective Init Time1.540s
Effective Time MeasureCPU
Mapping Time (Wall)54.158s
Mapping Time (CPU)117.560s
Mapping Time (CPU User)112.856s
Mapping Time (CPU System)4.704s
Init Time (Wall)1.638s
Init Time (CPU)1.540s
Init Time (CPU User)0.132s
Init Time (CPU System)1.408s
Additional Information
Mapper Memory Usage1919 MB
Total Test Runtime (Wall)74.658s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Gallus_gallus.fa 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/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwasw.sam
memory1796972000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq
[main] Real time: 1.563 sec; CPU: 1.480 sec
systime1.388
time1.58353495598
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwasw.sam
memory1795508000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq
[main] Real time: 1.609 sec; CPU: 1.528 sec
systime1.408
time1.63847494125
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory1919828000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 100000 sequences/pairs (15000000 bp) ...
[bsw2_stat] infer the insert size distribution from 11794 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (195, 200, 204)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (177, 222)
[bsw2_stat] mean and std.dev: (199.55, 7.01)
[bsw2_stat] low and high boundaries for proper pairs: (168, 231)
[bsw2_pair] #fixed=0, #rescued=2, #moved=0
[bsw2_stat] infer the insert size distribution from 11809 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (195, 200, 204)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (177, 222)
[bsw2_stat] mean and std.dev: (199.59, 6.94)
[bsw2_stat] low and high boundaries for proper pairs: (168, 231)
[bsw2_pair] #fixed=0, #rescued=0, #moved=0
[bsw2_stat] infer the insert size distribution from 11788 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (195, 200, 204)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (177, 222)
[bsw2_stat] mean and std.dev: (199.64, 6.90)
[bsw2_stat] low and high boundaries for proper pairs: (168, 231)
[bsw2_pair] #fixed=0, #rescued=1, #moved=0
[bsw2_stat] infer the insert size distribution from 11820 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (195, 200, 204)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (177, 222)
[bsw2_stat] mean and std.dev: (199.69, 6.90)
[bsw2_stat] low and high boundaries for proper pairs: (168, 231)
[bsw2_pair] #fixed=0, #rescued=0, #moved=0
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq reads2.fastq
[main] Real time: 54.129 sec; CPU: 117.540 sec
systime4.704
time54.1578941345
usrtime112.856
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a