breseq  version 0.38.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsUnknown_CH607-002R0006_good_1.fq3,786,198566,535,833100.0%149.6 bases150 bases94.8%
total3,786,198566,535,833100.0%149.6 bases150 bases94.8%

Reference Sequence Information

seq idlengthfit meanfit relative_variance% mapped readsdescription
coveragedistributionXen36_1648,837151.64.918.4%na
coveragedistributionXen36_2401,342140.43.410.5%na
coveragedistributionXen36_3250,908212.74.39.9%na
coveragedistributionXen36_4214,555210.93.98.4%na
coveragedistributionXen36_5192,873238.84.18.5%na
coveragedistributionXen36_6167,259174.25.55.5%na
coveragedistributionXen36_7133,618246.84.26.1%na
coveragedistributionXen36_8127,589123.12.72.9%na
coveragedistributionXen36_9124,450192.73.44.5%na
coveragedistributionXen36_10106,197182.03.63.6%na
coveragedistributionXen36_1174,743231.04.03.2%na
coveragedistributionXen36_1252,431191.94.01.9%na
coveragedistributionXen36_1350,485224.04.52.1%na
coveragedistributionXen36_1447,761184.33.41.6%na
coveragedistributionXen36_1537,893199.53.31.4%na
coveragedistributionXen36_1636,148161.44.01.0%na
coveragedistributionXen36_1723,721584.414.22.5%na
coveragedistributionXen36_1820,963124.73.60.5%na
coveragedistributionXen36_198,0891785.2197.02.4%na
coveragedistributionXen36_207,8891261.927.51.8%na
coveragedistributionXen36_217,351148.72.30.2%na
coveragedistributionXen36_225,249780.25.60.7%na
coveragedistributionXen36_234,747560.911.20.5%na
coveragedistributionXen36_244,540203.63.40.2%na
coveragedistributionXen36_254,177699.49.90.5%na
coveragedistributionXen36_263,519161.21.60.1%na
coveragedistributionXen36_272,102795.14.60.3%na
coveragedistributionXen36_281,675832.38.30.2%na
coveragedistributionXen36_291,304861.420.10.2%na
coveragedistributionXen36_301,218700.43.00.3%na
coveragedistributionXen36_311,209720.03.80.1%na
coveragedistributionXen36_321,019[859.7][44.4]0.2%na
coveragedistributionXen36_33668121.71.30.0%na
coveragedistributionXen36_34443109.81.70.0%na
total2,766,972100.0%

fit relative_variance 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.

Fit failed Negative binomial fit failed for this reference sequence. It may have an unusual coverage depth distribution. JC and MC predictions may be less accurate.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000039979
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 5
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000793
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.091

Junction Skew Score Calculation

reference sequencepr(no read start)
Xen36_10.70658
Xen36_20.72431
Xen36_30.62351
Xen36_40.62769
Xen36_50.59334
Xen36_60.67252
Xen36_70.58192
Xen36_80.75148
Xen36_90.64949
Xen36_100.66245
Xen36_110.59966
Xen36_120.64956
Xen36_130.61042
Xen36_140.66151
Xen36_150.63943
Xen36_160.70552
Xen36_170.35928
Xen36_180.75227
Xen36_190.11961
Xen36_200.15167
Xen36_210.72255
Xen36_220.27596
Xen36_230.36927
Xen36_240.64154
Xen36_250.35241
Xen36_260.70432
Xen36_270.28853
Xen36_280.29642
Xen36_290.33972
Xen36_300.24709
Xen36_310.35939
Xen36_32NA
Xen36_330.80389
Xen36_340.84763

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
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction0.1
Junction allow suboptimal matchesFALSE
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 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
bowtie2s.2023.01/rocky8/x86_64/amd/zen3/software/Bowtie2/2.4.5-GCC-11.3.0/bin/bowtie2-align-s
R4.2.1

Execution Times

stepstartendelapsed
Read and reference sequence file input22:52:52 30 Oct 202422:53:47 30 Oct 202455 seconds
Read alignment to reference genome22:53:47 30 Oct 202422:55:31 30 Oct 20241 minute 44 seconds
Preprocessing alignments for candidate junction identification22:55:32 30 Oct 202422:56:10 30 Oct 202438 seconds
Preliminary analysis of coverage distribution22:56:10 30 Oct 202422:57:54 30 Oct 20241 minute 44 seconds
Identifying junction candidates22:57:55 30 Oct 202422:59:57 30 Oct 20242 minutes 2 seconds
Re-alignment to junction candidates22:59:57 30 Oct 202423:00:38 30 Oct 202441 seconds
Resolving best read alignments23:00:38 30 Oct 202423:01:47 30 Oct 20241 minute 9 seconds
Creating BAM files23:01:47 30 Oct 202423:02:34 30 Oct 202447 seconds
Tabulating error counts23:02:34 30 Oct 202423:03:42 30 Oct 20241 minute 8 seconds
Re-calibrating base error rates23:03:42 30 Oct 202423:04:25 30 Oct 202443 seconds
Examining read alignment evidence23:04:25 30 Oct 202423:11:17 30 Oct 20246 minutes 52 seconds
Polymorphism statistics23:11:17 30 Oct 202423:11:18 30 Oct 20241 second
Output23:11:18 30 Oct 202423:11:24 30 Oct 20246 seconds
Output :: Mutation Prediction23:11:18 30 Oct 202423:11:19 30 Oct 20241 second
Output :: Mutation Annotation23:11:19 30 Oct 202423:11:20 30 Oct 20241 second
Total 18 minutes 32 seconds