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 Mapped29321598.01%
Wrongly Mapped59511.989%
Not Mapped20.001%
Total299168100.0%
Read Failure Statistics
Not mapped20.001%
Missing in mapper output00.0%
Mapped to wrong chromosome19490.651%
Mapped to wrong position40021.338%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment2
Secondary Alignments0
F-Measure0.990000
Precision0.980100
Recall1.000000
Timing
Raw Mapping Time152.528s
Effective Mapping Time152.324s
Effective Init Time0.204s
Effective Time MeasureCPU
Mapping Time (Wall)47.638s
Mapping Time (CPU)152.528s
Mapping Time (CPU User)147.760s
Mapping Time (CPU System)4.768s
Init Time (Wall)0.259s
Init Time (CPU)0.204s
Init Time (CPU User)0.012s
Init Time (CPU System)0.192s
Additional Information
Mapper Memory Usage529 MB
Total Test Runtime (Wall)89.483s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory209232000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.253 sec; CPU: 0.192 sec
systime0.188
time0.279581069946
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory209228000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.229 sec; CPU: 0.192 sec
systime0.192
time0.259330034256
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory529832000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 299168 sequences/pairs (29916800 bp) ...
[bsw2_stat] infer the insert size distribution from 32523 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 400, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (287, 512)
[bsw2_stat] mean and std.dev: (399.50, 32.78)
[bsw2_stat] low and high boundaries for proper pairs: (242, 557)
[bsw2_pair] #fixed=5301, #rescued=41, #moved=122
[bsw2_stat] infer the insert size distribution from 32582 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 400, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (287, 512)
[bsw2_stat] mean and std.dev: (399.45, 32.95)
[bsw2_stat] low and high boundaries for proper pairs: (242, 557)
[bsw2_pair] #fixed=5399, #rescued=56, #moved=156
[bsw2_stat] infer the insert size distribution from 32617 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (377, 399, 422)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (287, 512)
[bsw2_stat] mean and std.dev: (399.54, 33.13)
[bsw2_stat] low and high boundaries for proper pairs: (242, 557)
[bsw2_pair] #fixed=5404, #rescued=49, #moved=133
[bsw2_stat] infer the insert size distribution from 32411 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: (399.27, 32.82)
[bsw2_stat] low and high boundaries for proper pairs: (245, 553)
[bsw2_pair] #fixed=5483, #rescued=37, #moved=173
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq
[main] Real time: 47.594 sec; CPU: 152.496 sec
systime4.768
time47.6376719475
usrtime147.76
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300