breseq  version 0.35.0  revision fe39cd8f5880
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsV300044151_L1_B5GECOdqoRAAADAAA-520_1.fq4,160,865624,129,750100.0%150.0 bases150 bases85.2%
errorsV300044151_L1_B5GECOdqoRAAADAAA-520_2.fq4,160,865624,129,750100.0%150.0 bases150 bases84.9%
total8,321,7301,248,259,500100.0%150.0 bases150 bases85.0%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNODE_1414,005205.92.87.9%Genus species strain EcoliAnna.
coveragedistributionNODE_2248,152215.82.65.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3204,902223.62.94.3%Genus species strain EcoliAnna.
coveragedistributionNODE_4189,380210.92.73.7%Genus species strain EcoliAnna.
coveragedistributionNODE_5178,300245.72.94.1%Genus species strain EcoliAnna.
coveragedistributionNODE_6177,964236.93.43.9%Genus species strain EcoliAnna.
coveragedistributionNODE_7176,166264.13.54.4%Genus species strain EcoliAnna.
coveragedistributionNODE_8164,428222.72.73.4%Genus species strain EcoliAnna.
coveragedistributionNODE_9157,088240.32.73.5%Genus species strain EcoliAnna.
coveragedistributionNODE_10133,230240.93.03.1%Genus species strain EcoliAnna.
coveragedistributionNODE_11133,063228.03.22.8%Genus species strain EcoliAnna.
coveragedistributionNODE_12114,681240.63.22.6%Genus species strain EcoliAnna.
coveragedistributionNODE_13114,251215.02.62.3%Genus species strain EcoliAnna.
coveragedistributionNODE_14113,124251.63.32.7%Genus species strain EcoliAnna.
coveragedistributionNODE_15112,387249.02.92.6%Genus species strain EcoliAnna.
coveragedistributionNODE_16107,910206.22.62.1%Genus species strain EcoliAnna.
coveragedistributionNODE_17104,175247.63.52.4%Genus species strain EcoliAnna.
coveragedistributionNODE_1886,564236.33.61.9%Genus species strain EcoliAnna.
coveragedistributionNODE_1967,374215.73.71.4%Genus species strain EcoliAnna.
coveragedistributionNODE_2066,961224.23.91.4%Genus species strain EcoliAnna.
coveragedistributionNODE_2166,680224.02.81.4%Genus species strain EcoliAnna.
coveragedistributionNODE_2266,175253.63.11.6%Genus species strain EcoliAnna.
coveragedistributionNODE_2360,911204.32.91.2%Genus species strain EcoliAnna.
coveragedistributionNODE_2458,944254.82.21.4%Genus species strain EcoliAnna.
coveragedistributionNODE_2558,798272.62.81.5%Genus species strain EcoliAnna.
coveragedistributionNODE_2657,838245.23.41.3%Genus species strain EcoliAnna.
coveragedistributionNODE_2754,089271.43.81.4%Genus species strain EcoliAnna.
coveragedistributionNODE_2853,850259.83.41.3%Genus species strain EcoliAnna.
coveragedistributionNODE_2946,324239.32.41.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3045,367232.03.01.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3143,851215.13.00.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3241,346237.82.90.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3341,323258.62.81.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3441,175266.63.51.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3540,913239.03.10.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3640,204228.54.20.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3737,730201.62.00.7%Genus species strain EcoliAnna.
coveragedistributionNODE_3835,227248.63.20.8%Genus species strain EcoliAnna.
coveragedistributionNODE_3935,183223.43.30.7%Genus species strain EcoliAnna.
coveragedistributionNODE_4033,992252.84.10.8%Genus species strain EcoliAnna.
coveragedistributionNODE_4133,449225.02.60.7%Genus species strain EcoliAnna.
coveragedistributionNODE_4233,383205.42.00.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4333,326204.02.80.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4431,623212.23.20.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4531,140253.43.10.7%Genus species strain EcoliAnna.
coveragedistributionNODE_4630,887250.42.50.7%Genus species strain EcoliAnna.
coveragedistributionNODE_4726,798231.93.00.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4826,706267.33.80.7%Genus species strain EcoliAnna.
coveragedistributionNODE_4925,569250.32.80.6%Genus species strain EcoliAnna.
coveragedistributionNODE_5024,737205.62.40.5%Genus species strain EcoliAnna.
coveragedistributionNODE_5123,981245.46.90.5%Genus species strain EcoliAnna.
coveragedistributionNODE_5223,639231.52.50.5%Genus species strain EcoliAnna.
coveragedistributionNODE_5321,980272.62.70.6%Genus species strain EcoliAnna.
coveragedistributionNODE_5414,627211.72.40.3%Genus species strain EcoliAnna.
coveragedistributionNODE_5514,553205.24.30.3%Genus species strain EcoliAnna.
coveragedistributionNODE_5613,123282.72.20.3%Genus species strain EcoliAnna.
coveragedistributionNODE_5712,883251.23.20.3%Genus species strain EcoliAnna.
coveragedistributionNODE_5810,662209.42.70.2%Genus species strain EcoliAnna.
coveragedistributionNODE_599,269236.13.90.2%Genus species strain EcoliAnna.
coveragedistributionNODE_608,099257.65.50.2%Genus species strain EcoliAnna.
coveragedistributionNODE_617,785279.44.10.2%Genus species strain EcoliAnna.
coveragedistributionNODE_627,532214.25.80.1%Genus species strain EcoliAnna.
coveragedistributionNODE_636,704249.63.90.1%Genus species strain EcoliAnna.
coveragedistributionNODE_644,672247.81.60.1%Genus species strain EcoliAnna.
coveragedistributionNODE_654,267262.82.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_664,232229.31.50.1%Genus species strain EcoliAnna.
coveragedistributionNODE_673,549229.72.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_683,217258.61.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_693,083238.93.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_702,9361797.420.60.5%Genus species strain EcoliAnna.
coveragedistributionNODE_712,870222.82.00.1%Genus species strain EcoliAnna.
coveragedistributionNODE_722,572233.65.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_732,343233.83.80.0%Genus species strain EcoliAnna.
coveragedistributionNODE_742,071447.71.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_751,794226.23.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_761,792227.86.40.0%Genus species strain EcoliAnna.
coveragedistributionNODE_771,765265.02.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_781,7021679.836.50.2%Genus species strain EcoliAnna.
coveragedistributionNODE_791,696297.11.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_801,345747.41.90.1%Genus species strain EcoliAnna.
coveragedistributionNODE_811,255948.96.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_821,133339.91.70.0%Genus species strain EcoliAnna.
coveragedistributionNODE_831,1243048.89.00.2%Genus species strain EcoliAnna.
coveragedistributionNODE_841,117660.21.70.1%Genus species strain EcoliAnna.
coveragedistributionNODE_851,048[198.9][18.2]0.0%Genus species strain EcoliAnna.
coveragedistributionNODE_861,031479.11.90.0%Genus species strain EcoliAnna.
coveragedistributionNODE_87970155.82.80.0%Genus species strain EcoliAnna.
coveragedistributionNODE_88848367.36.30.0%Genus species strain EcoliAnna.
coveragedistributionNODE_89813678.113.20.0%Genus species strain EcoliAnna.
coveragedistributionNODE_90734544.03.20.0%Genus species strain EcoliAnna.
coveragedistributionNODE_917061972.12.90.1%Genus species strain EcoliAnna.
coveragedistributionNODE_92680651.415.90.0%Genus species strain EcoliAnna.
coveragedistributionNODE_93667811.030.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_94576[1606.7][46.1]0.1%Genus species strain EcoliAnna.
coveragedistributionNODE_95566771.66.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_96556383.02.80.0%Genus species strain EcoliAnna.
coveragedistributionNODE_97556206.21.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_98531392.51.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_99417[143.7][28.1]0.0%Genus species strain EcoliAnna.
total4,557,714100.0%

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.

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≤ 10000035047
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 ≤ 50001252
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.084

Junction Skew Score Calculation

reference sequencepr(no read start)
NODE_10.53738
NODE_20.52127
NODE_30.51392
NODE_40.53071
NODE_50.47937
NODE_60.49074
NODE_70.45333
NODE_80.51181
NODE_90.48776
NODE_100.48661
NODE_110.50630
NODE_120.48728
NODE_130.52614
NODE_140.47060
NODE_150.47522
NODE_160.53481
NODE_170.47968
NODE_180.49424
NODE_190.52510
NODE_200.51342
NODE_210.51172
NODE_220.47034
NODE_230.53864
NODE_240.46895
NODE_250.44554
NODE_260.48099
NODE_270.44800
NODE_280.45966
NODE_290.49120
NODE_300.49987
NODE_310.52260
NODE_320.49007
NODE_330.46602
NODE_340.45549
NODE_350.48919
NODE_360.50437
NODE_370.54275
NODE_380.48126
NODE_390.51187
NODE_400.47210
NODE_410.50742
NODE_420.53391
NODE_430.54162
NODE_440.52822
NODE_450.46951
NODE_460.47403
NODE_470.49892
NODE_480.45280
NODE_490.47760
NODE_500.53950
NODE_510.48609
NODE_520.50660
NODE_530.45114
NODE_540.52875
NODE_550.54146
NODE_560.42528
NODE_570.48277
NODE_580.54436
NODE_590.49995
NODE_600.46691
NODE_610.45080
NODE_620.53678
NODE_630.48561
NODE_640.47606
NODE_650.46660
NODE_660.49853
NODE_670.51691
NODE_680.47560
NODE_690.52027
NODE_700.05978
NODE_710.52574
NODE_720.52605
NODE_730.52582
NODE_740.32279
NODE_750.55379
NODE_760.51172
NODE_770.48697
NODE_780.10811
NODE_790.38503
NODE_800.21933
NODE_810.19522
NODE_820.41880
NODE_830.19386
NODE_840.25649
NODE_85NA
NODE_860.36178
NODE_870.67938
NODE_880.46993
NODE_890.32657
NODE_900.36512
NODE_910.20113
NODE_920.38676
NODE_930.31484
NODE_94NA
NODE_950.32420
NODE_960.57160
NODE_970.68025
NODE_980.48399
NODE_99NA

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
bowtie22.3.4.3
R3.6.1

Execution Times

stepstartendelapsed
Read and reference sequence file input13:46:08 05 Mar 202013:48:17 05 Mar 20202 minutes 9 seconds
Read alignment to reference genome13:48:17 05 Mar 202013:51:15 05 Mar 20202 minutes 58 seconds
Preprocessing alignments for candidate junction identification13:51:15 05 Mar 202013:52:50 05 Mar 20201 minute 35 seconds
Preliminary analysis of coverage distribution13:52:50 05 Mar 202013:58:42 05 Mar 20205 minutes 52 seconds
Identifying junction candidates13:58:42 05 Mar 202014:10:37 05 Mar 202011 minutes 55 seconds
Re-alignment to junction candidates14:10:37 05 Mar 202014:11:58 05 Mar 20201 minute 21 seconds
Resolving best read alignments14:11:58 05 Mar 202014:14:45 05 Mar 20202 minutes 47 seconds
Creating BAM files14:14:45 05 Mar 202014:18:24 05 Mar 20203 minutes 39 seconds
Tabulating error counts14:18:24 05 Mar 202014:20:11 05 Mar 20201 minute 47 seconds
Re-calibrating base error rates14:20:11 05 Mar 202014:21:39 05 Mar 20201 minute 28 seconds
Examining read alignment evidence14:21:39 05 Mar 202014:44:21 05 Mar 202022 minutes 42 seconds
Polymorphism statistics14:44:21 05 Mar 202014:44:24 05 Mar 20203 seconds
Output14:44:24 05 Mar 202014:46:24 05 Mar 20202 minutes 0 seconds
Total 1 hour 16 seconds