breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsPputida_PALE__HGL_Pputida_148_S136_L001_R1_001.good.fq8,038,4451,137,017,631100.0%141.4 bases150 bases94.2%
errorsPputida_PALE__HGL_Pputida_148_S136_L001_R2_001.good.fq8,038,4451,137,017,631100.0%141.4 bases150 bases93.6%
total16,076,8902,274,035,262100.0%141.4 bases150 bases93.9%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0029476,183,858342.96.0100.0%na
total6,183,858100.0%

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≤ 100000100000
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 3
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000494
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_0029470.44528

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 cutoff0.75
Consensus minimum variant coverage each strandOFF
Consensus minimum total coverage each strandOFF
Consensus minimum variant coverageOFF
Consensus minimum total coverageOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum variant coverage each strandOFF
Polymorphism minimum total coverage each strandOFF
Polymorphism minimum variant coverageOFF
Polymorphism minimum total coverageOFF
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

Software Versions

programversion
bowtie22.3.4.1
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input03:06:53 08 Apr 202003:13:11 08 Apr 20206 minutes 18 seconds
Read alignment to reference genome03:13:12 08 Apr 202003:49:42 08 Apr 202036 minutes 30 seconds
Preprocessing alignments for candidate junction identification03:49:42 08 Apr 202003:58:46 08 Apr 20209 minutes 4 seconds
Preliminary analysis of coverage distribution03:58:46 08 Apr 202004:06:41 08 Apr 20207 minutes 55 seconds
Identifying junction candidates04:06:41 08 Apr 202004:08:52 08 Apr 20202 minutes 11 seconds
Re-alignment to junction candidates04:08:52 08 Apr 202004:17:45 08 Apr 20208 minutes 53 seconds
Resolving best read alignments04:17:45 08 Apr 202004:29:54 08 Apr 202012 minutes 9 seconds
Creating BAM files04:29:54 08 Apr 202004:35:46 08 Apr 20205 minutes 52 seconds
Tabulating error counts04:35:46 08 Apr 202004:41:45 08 Apr 20205 minutes 59 seconds
Re-calibrating base error rates04:41:45 08 Apr 202004:41:47 08 Apr 20202 seconds
Examining read alignment evidence04:41:47 08 Apr 202005:28:55 08 Apr 202047 minutes 8 seconds
Polymorphism statistics05:28:55 08 Apr 202005:29:18 08 Apr 202023 seconds
Output05:29:18 08 Apr 202005:30:43 08 Apr 20201 minute 25 seconds
Total 2 hours 23 minutes 49 seconds