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 Mapped14716598.11%
Wrongly Mapped28341.889%
Not Mapped10.001%
Total150000100.0%
Read Failure Statistics
Not mapped10.001%
Missing in mapper output00.0%
Mapped to wrong chromosome23551.57%
Mapped to wrong position4790.319%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment5
Secondary Alignments0
F-Measure0.990500
Precision0.981100
Recall1.000000
Timing
Raw Mapping Time79.069s
Effective Mapping Time79.038s
Effective Init Time0.031s
Effective Time MeasureCPU
Mapping Time (Wall)24.896s
Mapping Time (CPU)79.069s
Mapping Time (CPU User)78.597s
Mapping Time (CPU System)0.472s
Init Time (Wall)0.064s
Init Time (CPU)0.031s
Init Time (CPU User)0.003s
Init Time (CPU System)0.028s
Additional Information
Mapper Memory Usage174 MB
Total Test Runtime (Wall)33.285s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Cryptosporidium.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/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory33888000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq
[main] Real time: 0.061 sec; CPU: 0.028 sec
systime0.028995
time0.0671300888062
usrtime0.002999
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory33892000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq
[main] Real time: 0.057 sec; CPU: 0.027 sec
systime0.027995
time0.0638251304626
usrtime0.002999
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Cryptosporidium.fasta reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory174052000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 150000 sequences/pairs (15000000 bp) ...
[bsw2_stat] infer the insert size distribution from 17934 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 122, 138)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 194)
[bsw2_stat] mean and std.dev: (125.79, 19.30)
[bsw2_stat] low and high boundaries for proper pairs: (100, 222)
[bsw2_pair] #fixed=1482, #rescued=10, #moved=0
[bsw2_stat] infer the insert size distribution from 17883 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 122, 137)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 191)
[bsw2_stat] mean and std.dev: (125.63, 19.05)
[bsw2_stat] low and high boundaries for proper pairs: (100, 218)
[bsw2_pair] #fixed=1431, #rescued=11, #moved=1
[bsw2_stat] infer the insert size distribution from 17839 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 121, 137)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 191)
[bsw2_stat] mean and std.dev: (125.43, 18.97)
[bsw2_stat] low and high boundaries for proper pairs: (100, 218)
[bsw2_pair] #fixed=1398, #rescued=14, #moved=3
[bsw2_stat] infer the insert size distribution from 17878 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (110, 122, 137)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (100, 191)
[bsw2_stat] mean and std.dev: (125.51, 18.93)
[bsw2_stat] low and high boundaries for proper pairs: (100, 218)
[bsw2_pair] #fixed=1468, #rescued=9, #moved=3
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads1.fastq reads2.fastq
[main] Real time: 24.884 sec; CPU: 79.060 sec
systime0.471928
time24.8955569267
usrtime78.597051
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae