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 Mapped32227490.588%
Wrongly Mapped334599.405%
Not Mapped230.006%
Total355756100.0%
Read Failure Statistics
Not mapped230.006%
Missing in mapper output00.0%
Mapped to wrong chromosome181695.107%
Mapped to wrong position152904.298%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.950600
Precision0.905900
Recall0.999900
Timing
Raw Mapping Time124.988s
Effective Mapping Time124.412s
Effective Init Time0.576s
Effective Time MeasureCPU
Mapping Time (Wall)41.760s
Mapping Time (CPU)124.988s
Mapping Time (CPU User)123.076s
Mapping Time (CPU System)1.912s
Init Time (Wall)0.569s
Init Time (CPU)0.576s
Init Time (CPU User)0.120s
Init Time (CPU System)0.456s
Additional Information
Mapper Memory Usage261 MB
Total Test Runtime (Wall)128.457s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory224252000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime0.484
time16.1076509953
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory221412000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime0.456
time0.568878889084
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory261080000
return0
status1
stderr
None
stdout
177878 reads; of these:
177878 (100.00%) were paired; of these:
89050 (50.06%) aligned concordantly 0 times
72575 (40.80%) aligned concordantly exactly 1 time
16253 (9.14%) aligned concordantly >1 times
----
89050 pairs aligned concordantly 0 times; of these:
73715 (82.78%) aligned discordantly 1 time
----
15335 pairs aligned 0 times concordantly or discordantly; of these:
30670 mates make up the pairs; of these:
23 (0.07%) aligned 0 times
771 (2.51%) aligned exactly 1 time
29876 (97.41%) aligned >1 times
99.99% overall alignment rate
systime1.912
time41.7601089478
usrtime123.076
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517