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 Mapped32154790.384%
Wrongly Mapped342049.614%
Not Mapped50.001%
Total355756100.0%
Read Failure Statistics
Not mapped50.001%
Missing in mapper output00.0%
Mapped to wrong chromosome195455.494%
Mapped to wrong position146594.121%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment29
Secondary Alignments0
F-Measure0.949500
Precision0.903900
Recall1.000000
Timing
Raw Mapping Time208.488s
Effective Mapping Time208.252s
Effective Init Time0.236s
Effective Time MeasureCPU
Mapping Time (Wall)66.005s
Mapping Time (CPU)208.488s
Mapping Time (CPU User)203.032s
Mapping Time (CPU System)5.456s
Init Time (Wall)0.298s
Init Time (CPU)0.236s
Init Time (CPU User)0.012s
Init Time (CPU System)0.224s
Additional Information
Mapper Memory Usage628 MB
Total Test Runtime (Wall)118.921s
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
memory248772000
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: 0.273 sec; CPU: 0.232 sec
systime0.22
time0.302402019501
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/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
memory250284000
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: 0.268 sec; CPU: 0.228 sec
systime0.224
time0.297545909882
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/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
memory628904000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 355756 sequences/pairs (35931356 bp) ...
[bsw2_stat] infer the insert size distribution from 36848 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (111, 123, 138)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (101, 192)
[bsw2_stat] mean and std.dev: (126.49, 18.91)
[bsw2_stat] low and high boundaries for proper pairs: (101, 219)
[bsw2_pair] #fixed=3875, #rescued=47, #moved=21
[bsw2_stat] infer the insert size distribution from 36935 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (111, 123, 139)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (101, 195)
[bsw2_stat] mean and std.dev: (126.76, 19.11)
[bsw2_stat] low and high boundaries for proper pairs: (101, 223)
[bsw2_pair] #fixed=3856, #rescued=58, #moved=19
[bsw2_stat] infer the insert size distribution from 37002 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (111, 123, 138)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (101, 192)
[bsw2_stat] mean and std.dev: (126.51, 18.92)
[bsw2_stat] low and high boundaries for proper pairs: (101, 219)
[bsw2_pair] #fixed=3773, #rescued=51, #moved=15
[bsw2_stat] infer the insert size distribution from 36830 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (111, 123, 138)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (101, 192)
[bsw2_stat] mean and std.dev: (126.39, 18.88)
[bsw2_stat] low and high boundaries for proper pairs: (101, 219)
[bsw2_pair] #fixed=3868, #rescued=43, #moved=13
[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: 65.955 sec; CPU: 208.444 sec
systime5.456
time66.0054738522
usrtime203.032
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517