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 Mapped9906699.066%
Wrongly Mapped9340.934%
Not Mapped00.0%
Total100000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome7340.734%
Mapped to wrong position2000.2%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment1
Secondary Alignments0
F-Measure0.995300
Precision0.990700
Recall1.000000
Timing
Raw Mapping Time85.720s
Effective Mapping Time85.668s
Effective Init Time0.052s
Effective Time MeasureCPU
Mapping Time (Wall)36.892s
Mapping Time (CPU)85.720s
Mapping Time (CPU User)84.368s
Mapping Time (CPU System)1.352s
Init Time (Wall)6.414s
Init Time (CPU)0.052s
Init Time (CPU User)0.008s
Init Time (CPU System)0.044s
Additional Information
Mapper Memory Usage144 MB
Total Test Runtime (Wall)88.034s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 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/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory25856000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 5.881 sec; CPU: 0.044 sec
systime0.044
time7.48834204674
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory25848000
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/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 4.989 sec; CPU: 0.044 sec
systime0.044
time6.41377401352
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory144780000
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 12003 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (376, 398, 421)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (286, 511)
[bsw2_stat] mean and std.dev: (398.86, 33.46)
[bsw2_stat] low and high boundaries for proper pairs: (241, 556)
[bsw2_pair] #fixed=2542, #rescued=30, #moved=7
[bsw2_stat] infer the insert size distribution from 12060 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 400, 423)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (285, 515)
[bsw2_stat] mean and std.dev: (399.74, 33.60)
[bsw2_stat] low and high boundaries for proper pairs: (239, 561)
[bsw2_pair] #fixed=2647, #rescued=12, #moved=3
[bsw2_stat] infer the insert size distribution from 12045 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (376, 399, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (284, 514)
[bsw2_stat] mean and std.dev: (398.88, 33.66)
[bsw2_stat] low and high boundaries for proper pairs: (238, 560)
[bsw2_pair] #fixed=2477, #rescued=16, #moved=10
[bsw2_stat] infer the insert size distribution from 11995 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 399, 421)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (289, 509)
[bsw2_stat] mean and std.dev: (399.12, 32.98)
[bsw2_stat] low and high boundaries for proper pairs: (245, 553)
[bsw2_pair] #fixed=2616, #rescued=19, #moved=12
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq
[main] Real time: 35.823 sec; CPU: 85.712 sec
systime1.352
time36.8921978474
usrtime84.368
working_directory/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f