breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsALE-IL7_S7_L002_R2_0011,725,131259,673,75699.5%150.5 bases151 bases96.0%
errorsALE-IL7_S7_L003_R1_0011,758,837264,767,40299.8%150.5 bases151 bases99.1%
errorsALE-IL7_S7_L004_R1_0011,753,382263,956,20499.8%150.5 bases151 bases99.2%
errorsALE-IL7_S7_L001_R1_0011,734,381261,054,08399.6%150.5 bases151 bases99.3%
errorsALE-IL7_S7_L003_R2_0011,755,455264,227,25599.6%150.5 bases151 bases95.6%
errorsALE-IL7_S7_L001_R2_0011,732,265260,730,93599.5%150.5 bases151 bases96.0%
errorsALE-IL7_S7_L004_R2_0011,748,886263,260,81799.6%150.5 bases151 bases96.2%
errorsALE-IL7_S7_L002_R1_0011,727,330260,012,37899.6%150.5 bases151 bases99.3%
total13,935,6672,097,682,83099.6%150.5 bases151 bases97.6%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652441.73.7100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000016239
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000379
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.025

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.33219

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Execution Times

stepstartendelapsed
Read and reference sequence file input00:28:36 22 Apr 201600:34:28 22 Apr 20165 minutes 52 seconds
Read alignment to reference genome00:34:28 22 Apr 201600:53:29 22 Apr 201619 minutes 1 second
Preprocessing alignments for candidate junction identification00:53:29 22 Apr 201601:01:10 22 Apr 20167 minutes 41 seconds
Preliminary analysis of coverage distribution01:01:10 22 Apr 201601:15:33 22 Apr 201614 minutes 23 seconds
Identifying junction candidates01:15:33 22 Apr 201601:15:37 22 Apr 20164 seconds
Re-alignment to junction candidates01:15:37 22 Apr 201601:19:10 22 Apr 20163 minutes 33 seconds
Resolving alignments with junction candidates01:19:10 22 Apr 201601:38:56 22 Apr 201619 minutes 46 seconds
Creating BAM files01:38:56 22 Apr 201601:48:45 22 Apr 20169 minutes 49 seconds
Tabulating error counts01:48:45 22 Apr 201602:07:54 22 Apr 201619 minutes 9 seconds
Re-calibrating base error rates02:07:54 22 Apr 201602:07:57 22 Apr 20163 seconds
Examining read alignment evidence02:07:57 22 Apr 201603:59:40 22 Apr 20161 hour 51 minutes 43 seconds
Polymorphism statistics03:59:40 22 Apr 201603:59:41 22 Apr 20161 second
Output03:59:42 22 Apr 201604:02:01 22 Apr 20162 minutes 19 seconds
Total 3 hours 33 minutes 24 seconds