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_B5GECOdqoRAAACAAA-519_1.fq4,154,622623,193,300100.0%150.0 bases150 bases99.6%
errorsV300044151_L1_B5GECOdqoRAAACAAA-519_2.fq4,154,622623,193,300100.0%150.0 bases150 bases99.4%
total8,309,2441,246,386,600100.0%150.0 bases150 bases99.5%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNODE_1414,005182.83.66.1%Genus species strain EcoliAnna.
coveragedistributionNODE_2248,152216.32.94.3%Genus species strain EcoliAnna.
coveragedistributionNODE_3204,902248.03.54.1%Genus species strain EcoliAnna.
coveragedistributionNODE_4189,380195.23.12.9%Genus species strain EcoliAnna.
coveragedistributionNODE_5178,300320.43.74.6%Genus species strain EcoliAnna.
coveragedistributionNODE_6177,964285.94.04.1%Genus species strain EcoliAnna.
coveragedistributionNODE_7176,166385.84.75.4%Genus species strain EcoliAnna.
coveragedistributionNODE_8164,428232.43.53.1%Genus species strain EcoliAnna.
coveragedistributionNODE_9157,088294.33.13.7%Genus species strain EcoliAnna.
coveragedistributionNODE_10133,230303.03.33.3%Genus species strain EcoliAnna.
coveragedistributionNODE_11133,063261.54.02.8%Genus species strain EcoliAnna.
coveragedistributionNODE_12114,681318.53.92.9%Genus species strain EcoliAnna.
coveragedistributionNODE_13114,251216.83.02.0%Genus species strain EcoliAnna.
coveragedistributionNODE_14113,124345.25.33.1%Genus species strain EcoliAnna.
coveragedistributionNODE_15112,387340.23.73.1%Genus species strain EcoliAnna.
coveragedistributionNODE_16107,910182.82.71.6%Genus species strain EcoliAnna.
coveragedistributionNODE_17104,175332.54.32.7%Genus species strain EcoliAnna.
coveragedistributionNODE_1886,564278.83.41.9%Genus species strain EcoliAnna.
coveragedistributionNODE_1967,374209.93.31.1%Genus species strain EcoliAnna.
coveragedistributionNODE_2066,961235.93.01.3%Genus species strain EcoliAnna.
coveragedistributionNODE_2166,680248.33.41.3%Genus species strain EcoliAnna.
coveragedistributionNODE_2266,175343.04.01.8%Genus species strain EcoliAnna.
coveragedistributionNODE_2360,911166.23.70.8%Genus species strain EcoliAnna.
coveragedistributionNODE_2458,944358.03.41.7%Genus species strain EcoliAnna.
coveragedistributionNODE_2558,798451.73.82.1%Genus species strain EcoliAnna.
coveragedistributionNODE_2657,838312.53.91.4%Genus species strain EcoliAnna.
coveragedistributionNODE_2754,089377.85.21.6%Genus species strain EcoliAnna.
coveragedistributionNODE_2853,850369.04.11.6%Genus species strain EcoliAnna.
coveragedistributionNODE_2946,324299.83.21.1%Genus species strain EcoliAnna.
coveragedistributionNODE_3045,367256.93.50.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3143,851208.63.10.7%Genus species strain EcoliAnna.
coveragedistributionNODE_3241,346287.33.80.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3341,323340.04.21.1%Genus species strain EcoliAnna.
coveragedistributionNODE_3441,175365.04.31.2%Genus species strain EcoliAnna.
coveragedistributionNODE_3540,913289.23.91.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3640,204262.64.10.8%Genus species strain EcoliAnna.
coveragedistributionNODE_3737,730168.51.90.5%Genus species strain EcoliAnna.
coveragedistributionNODE_3835,227349.42.81.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3935,183186.11.60.5%Genus species strain EcoliAnna.
coveragedistributionNODE_4033,992332.14.60.9%Genus species strain EcoliAnna.
coveragedistributionNODE_4133,449239.12.30.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4233,383175.02.50.5%Genus species strain EcoliAnna.
coveragedistributionNODE_4333,326177.92.60.5%Genus species strain EcoliAnna.
coveragedistributionNODE_4431,623209.83.10.5%Genus species strain EcoliAnna.
coveragedistributionNODE_4531,140334.84.20.8%Genus species strain EcoliAnna.
coveragedistributionNODE_4630,887346.23.00.9%Genus species strain EcoliAnna.
coveragedistributionNODE_4726,798262.83.60.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4826,706358.73.80.8%Genus species strain EcoliAnna.
coveragedistributionNODE_4925,569329.53.30.7%Genus species strain EcoliAnna.
coveragedistributionNODE_5024,737180.32.40.4%Genus species strain EcoliAnna.
coveragedistributionNODE_5123,981288.96.50.5%Genus species strain EcoliAnna.
coveragedistributionNODE_5223,639268.92.40.5%Genus species strain EcoliAnna.
coveragedistributionNODE_5321,980446.04.00.8%Genus species strain EcoliAnna.
coveragedistributionNODE_5414,627172.12.20.2%Genus species strain EcoliAnna.
coveragedistributionNODE_5514,553212.13.30.2%Genus species strain EcoliAnna.
coveragedistributionNODE_5613,123386.82.70.4%Genus species strain EcoliAnna.
coveragedistributionNODE_5712,883350.63.60.4%Genus species strain EcoliAnna.
coveragedistributionNODE_5810,662255.23.00.2%Genus species strain EcoliAnna.
coveragedistributionNODE_599,269268.83.50.2%Genus species strain EcoliAnna.
coveragedistributionNODE_608,099338.76.10.2%Genus species strain EcoliAnna.
coveragedistributionNODE_617,785463.82.80.3%Genus species strain EcoliAnna.
coveragedistributionNODE_627,532240.25.70.1%Genus species strain EcoliAnna.
coveragedistributionNODE_636,704276.35.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_644,672291.03.60.1%Genus species strain EcoliAnna.
coveragedistributionNODE_654,267384.92.60.1%Genus species strain EcoliAnna.
coveragedistributionNODE_664,232273.12.10.1%Genus species strain EcoliAnna.
coveragedistributionNODE_673,549216.61.10.1%Genus species strain EcoliAnna.
coveragedistributionNODE_683,217336.72.40.1%Genus species strain EcoliAnna.
coveragedistributionNODE_693,083245.74.80.1%Genus species strain EcoliAnna.
coveragedistributionNODE_702,9362403.88.90.5%Genus species strain EcoliAnna.
coveragedistributionNODE_712,870177.51.30.0%Genus species strain EcoliAnna.
coveragedistributionNODE_722,572262.73.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_732,343280.24.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_742,071376.74.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_751,794209.81.20.0%Genus species strain EcoliAnna.
coveragedistributionNODE_761,792212.73.70.0%Genus species strain EcoliAnna.
coveragedistributionNODE_771,765360.41.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_781,7022440.8119.60.3%Genus species strain EcoliAnna.
coveragedistributionNODE_791,696396.03.80.0%Genus species strain EcoliAnna.
coveragedistributionNODE_801,345826.55.10.1%Genus species strain EcoliAnna.
coveragedistributionNODE_811,2551034.018.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_821,133473.811.40.0%Genus species strain EcoliAnna.
coveragedistributionNODE_831,1243777.515.60.2%Genus species strain EcoliAnna.
coveragedistributionNODE_841,117760.81.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_851,048249.28.40.0%Genus species strain EcoliAnna.
coveragedistributionNODE_861,031698.11.10.1%Genus species strain EcoliAnna.
coveragedistributionNODE_87970135.11.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_88848343.51.20.0%Genus species strain EcoliAnna.
coveragedistributionNODE_89813835.411.50.0%Genus species strain EcoliAnna.
coveragedistributionNODE_90734695.15.70.0%Genus species strain EcoliAnna.
coveragedistributionNODE_917062195.844.70.1%Genus species strain EcoliAnna.
coveragedistributionNODE_92680911.164.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_93667983.624.70.0%Genus species strain EcoliAnna.
coveragedistributionNODE_94576[1779.8][44.2]0.1%Genus species strain EcoliAnna.
coveragedistributionNODE_95566927.23.40.0%Genus species strain EcoliAnna.
coveragedistributionNODE_96556495.41.40.0%Genus species strain EcoliAnna.
coveragedistributionNODE_97556181.51.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_98531459.41.90.0%Genus species strain EcoliAnna.
coveragedistributionNODE_99417230.61.80.0%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≤ 10000039987
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 ≤ 50001201
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.081

Junction Skew Score Calculation

reference sequencepr(no read start)
NODE_10.57501
NODE_20.52433
NODE_30.48185
NODE_40.55600
NODE_50.39360
NODE_60.43127
NODE_70.33082
NODE_80.50010
NODE_90.42215
NODE_100.41390
NODE_110.46456
NODE_120.39915
NODE_130.52715
NODE_140.36944
NODE_150.37610
NODE_160.57589
NODE_170.38386
NODE_180.44532
NODE_190.53728
NODE_200.49801
NODE_210.48191
NODE_220.37365
NODE_230.60501
NODE_240.35955
NODE_250.28375
NODE_260.40240
NODE_270.34116
NODE_280.34685
NODE_290.41978
NODE_300.46993
NODE_310.53538
NODE_320.42963
NODE_330.37551
NODE_340.34971
NODE_350.42718
NODE_360.46373
NODE_370.59991
NODE_380.37148
NODE_390.57190
NODE_400.38441
NODE_410.49399
NODE_420.58906
NODE_430.58390
NODE_440.54109
NODE_450.38379
NODE_460.36925
NODE_470.46233
NODE_480.35881
NODE_490.38725
NODE_500.58346
NODE_510.42972
NODE_520.45945
NODE_530.29695
NODE_540.59014
NODE_550.53942
NODE_560.32576
NODE_570.36822
NODE_580.48307
NODE_590.45841
NODE_600.38289
NODE_610.29807
NODE_620.51002
NODE_630.45547
NODE_640.44369
NODE_650.35318
NODE_660.46916
NODE_670.54029
NODE_680.39944
NODE_690.49367
NODE_700.05381
NODE_710.55549
NODE_720.49086
NODE_730.46244
NODE_740.37808
NODE_750.56438
NODE_760.52567
NODE_770.38102
NODE_780.09166
NODE_790.32030
NODE_800.19926
NODE_810.18048
NODE_820.33363
NODE_830.16748
NODE_840.22739
NODE_850.55534
NODE_860.26576
NODE_870.70670
NODE_880.47347
NODE_890.28413
NODE_900.33038
NODE_910.20751
NODE_920.34926
NODE_930.29085
NODE_94NA
NODE_950.30830
NODE_960.57165
NODE_970.75389
NODE_980.46328
NODE_990.65468

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 input13:46:01 05 Mar 202013:48:13 05 Mar 20202 minutes 12 seconds
Read alignment to reference genome13:48:13 05 Mar 202013:51:44 05 Mar 20203 minutes 31 seconds
Preprocessing alignments for candidate junction identification13:51:44 05 Mar 202013:53:32 05 Mar 20201 minute 48 seconds
Preliminary analysis of coverage distribution13:53:32 05 Mar 202014:00:07 05 Mar 20206 minutes 35 seconds
Identifying junction candidates14:00:07 05 Mar 202014:12:11 05 Mar 202012 minutes 4 seconds
Re-alignment to junction candidates14:12:11 05 Mar 202014:13:11 05 Mar 20201 minute 0 seconds
Resolving best read alignments14:13:11 05 Mar 202014:16:11 05 Mar 20203 minutes 0 seconds
Creating BAM files14:16:11 05 Mar 202014:20:21 05 Mar 20204 minutes 10 seconds
Tabulating error counts14:20:21 05 Mar 202014:22:28 05 Mar 20202 minutes 7 seconds
Re-calibrating base error rates14:22:28 05 Mar 202014:23:50 05 Mar 20201 minute 22 seconds
Examining read alignment evidence14:23:50 05 Mar 202014:49:50 05 Mar 202026 minutes 0 seconds
Polymorphism statistics14:49:50 05 Mar 202014:49:52 05 Mar 20202 seconds
Output14:49:52 05 Mar 202014:52:07 05 Mar 20202 minutes 15 seconds
Total 1 hour 6 minutes 6 seconds