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 Mapped63720288.669%
Wrongly Mapped7794410.846%
Not Mapped34820.485%
Total718628100.0%
Read Failure Statistics
Not mapped34820.485%
Missing in mapper output00.0%
Mapped to wrong chromosome465236.474%
Mapped to wrong position314214.372%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment2
Secondary Alignments0
F-Measure0.939900
Precision0.891000
Recall0.994600
Timing
Raw Mapping Time197.556s
Effective Mapping Time197.304s
Effective Init Time0.252s
Effective Time MeasureCPU
Mapping Time (Wall)76.486s
Mapping Time (CPU)197.556s
Mapping Time (CPU User)188.020s
Mapping Time (CPU System)9.536s
Init Time (Wall)0.394s
Init Time (CPU)0.252s
Init Time (CPU User)0.020s
Init Time (CPU System)0.232s
Additional Information
Mapper Memory Usage751 MB
Total Test Runtime (Wall)162.142s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248900000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.290 sec; CPU: 0.248 sec
systime0.24
time0.350746870041
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory248904000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.352 sec; CPU: 0.240 sec
systime0.232
time0.39421582222
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory751608000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 718628 sequences/pairs (35931400 bp) ...
[bsw2_stat] infer the insert size distribution from 65567 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (107, 129, 151)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (50, 239)
[bsw2_stat] mean and std.dev: (129.21, 32.43)
[bsw2_stat] low and high boundaries for proper pairs: (50, 283)
[bsw2_pair] #fixed=7512, #rescued=9454, #moved=1078
[bsw2_stat] infer the insert size distribution from 65677 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (107, 129, 151)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (50, 239)
[bsw2_stat] mean and std.dev: (129.40, 32.39)
[bsw2_stat] low and high boundaries for proper pairs: (50, 283)
[bsw2_pair] #fixed=7457, #rescued=9501, #moved=1060
[bsw2_stat] infer the insert size distribution from 65624 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (107, 129, 152)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (50, 242)
[bsw2_stat] mean and std.dev: (129.27, 32.66)
[bsw2_stat] low and high boundaries for proper pairs: (50, 287)
[bsw2_pair] #fixed=7257, #rescued=9522, #moved=1098
[bsw2_stat] infer the insert size distribution from 65788 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (107, 129, 151)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (50, 239)
[bsw2_stat] mean and std.dev: (129.23, 32.61)
[bsw2_stat] low and high boundaries for proper pairs: (50, 283)
[bsw2_pair] #fixed=7366, #rescued=9437, #moved=1019
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 76.442 sec; CPU: 197.528 sec
systime9.536
time76.4863159657
usrtime188.02
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6