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_B5GECOdqoRAAABAAA-518_1.fq4,154,025623,103,750100.0%150.0 bases150 bases99.4%
errorsV300044151_L1_B5GECOdqoRAAABAAA-518_2.fq4,154,025623,103,750100.0%150.0 bases150 bases99.2%
total8,308,0501,246,207,500100.0%150.0 bases150 bases99.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNODE_1414,005208.13.56.9%Genus species strain EcoliAnna.
coveragedistributionNODE_2248,152221.33.04.4%Genus species strain EcoliAnna.
coveragedistributionNODE_3204,902245.63.14.0%Genus species strain EcoliAnna.
coveragedistributionNODE_4189,380213.73.03.2%Genus species strain EcoliAnna.
coveragedistributionNODE_5178,300300.73.34.3%Genus species strain EcoliAnna.
coveragedistributionNODE_6177,964277.44.03.9%Genus species strain EcoliAnna.
coveragedistributionNODE_7176,166363.64.15.2%Genus species strain EcoliAnna.
coveragedistributionNODE_8164,428238.23.03.1%Genus species strain EcoliAnna.
coveragedistributionNODE_9157,088274.83.43.5%Genus species strain EcoliAnna.
coveragedistributionNODE_10133,230289.13.33.1%Genus species strain EcoliAnna.
coveragedistributionNODE_11133,063251.53.52.7%Genus species strain EcoliAnna.
coveragedistributionNODE_12114,681292.33.72.7%Genus species strain EcoliAnna.
coveragedistributionNODE_13114,251229.13.12.1%Genus species strain EcoliAnna.
coveragedistributionNODE_14113,124319.14.12.9%Genus species strain EcoliAnna.
coveragedistributionNODE_15112,387318.43.82.9%Genus species strain EcoliAnna.
coveragedistributionNODE_16107,910205.12.51.8%Genus species strain EcoliAnna.
coveragedistributionNODE_17104,175305.33.92.5%Genus species strain EcoliAnna.
coveragedistributionNODE_1886,564272.83.81.9%Genus species strain EcoliAnna.
coveragedistributionNODE_1967,374228.03.71.2%Genus species strain EcoliAnna.
coveragedistributionNODE_2066,961232.23.41.3%Genus species strain EcoliAnna.
coveragedistributionNODE_2166,680241.23.71.3%Genus species strain EcoliAnna.
coveragedistributionNODE_2266,175315.93.91.7%Genus species strain EcoliAnna.
coveragedistributionNODE_2360,911186.33.10.9%Genus species strain EcoliAnna.
coveragedistributionNODE_2458,944330.83.31.6%Genus species strain EcoliAnna.
coveragedistributionNODE_2558,798643.84.83.0%Genus species strain EcoliAnna.
coveragedistributionNODE_2657,838292.73.11.3%Genus species strain EcoliAnna.
coveragedistributionNODE_2754,089352.84.21.5%Genus species strain EcoliAnna.
coveragedistributionNODE_2853,850342.13.71.5%Genus species strain EcoliAnna.
coveragedistributionNODE_2946,324280.23.31.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3045,367253.63.60.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3143,851221.52.80.8%Genus species strain EcoliAnna.
coveragedistributionNODE_3241,346269.03.00.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3341,323314.62.91.0%Genus species strain EcoliAnna.
coveragedistributionNODE_3441,175342.44.61.1%Genus species strain EcoliAnna.
coveragedistributionNODE_3540,913267.93.00.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3640,204257.74.30.8%Genus species strain EcoliAnna.
coveragedistributionNODE_3737,730189.62.10.6%Genus species strain EcoliAnna.
coveragedistributionNODE_3835,227324.53.40.9%Genus species strain EcoliAnna.
coveragedistributionNODE_3935,183211.02.80.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4033,992311.04.70.8%Genus species strain EcoliAnna.
coveragedistributionNODE_4133,449232.92.60.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4233,383191.72.40.5%Genus species strain EcoliAnna.
coveragedistributionNODE_4333,326198.32.80.5%Genus species strain EcoliAnna.
coveragedistributionNODE_4431,623226.74.10.6%Genus species strain EcoliAnna.
coveragedistributionNODE_4531,140315.14.10.8%Genus species strain EcoliAnna.
coveragedistributionNODE_4630,887322.83.10.8%Genus species strain EcoliAnna.
coveragedistributionNODE_4726,798253.23.10.5%Genus species strain EcoliAnna.
coveragedistributionNODE_4826,706340.63.80.7%Genus species strain EcoliAnna.
coveragedistributionNODE_4925,569305.53.60.6%Genus species strain EcoliAnna.
coveragedistributionNODE_5024,737199.12.50.4%Genus species strain EcoliAnna.
coveragedistributionNODE_5123,981281.27.10.5%Genus species strain EcoliAnna.
coveragedistributionNODE_5223,639258.12.70.5%Genus species strain EcoliAnna.
coveragedistributionNODE_5321,980634.43.31.1%Genus species strain EcoliAnna.
coveragedistributionNODE_5414,627195.02.40.2%Genus species strain EcoliAnna.
coveragedistributionNODE_5514,553220.54.30.3%Genus species strain EcoliAnna.
coveragedistributionNODE_5613,123364.62.90.4%Genus species strain EcoliAnna.
coveragedistributionNODE_5712,883325.43.80.3%Genus species strain EcoliAnna.
coveragedistributionNODE_5810,662238.62.90.2%Genus species strain EcoliAnna.
coveragedistributionNODE_599,269259.63.90.2%Genus species strain EcoliAnna.
coveragedistributionNODE_608,099322.27.20.2%Genus species strain EcoliAnna.
coveragedistributionNODE_617,785668.34.70.4%Genus species strain EcoliAnna.
coveragedistributionNODE_627,532230.33.40.1%Genus species strain EcoliAnna.
coveragedistributionNODE_636,704272.13.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_644,672281.91.80.1%Genus species strain EcoliAnna.
coveragedistributionNODE_654,267329.72.70.1%Genus species strain EcoliAnna.
coveragedistributionNODE_664,232260.31.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_673,549231.31.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_683,217310.63.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_693,083249.92.40.1%Genus species strain EcoliAnna.
coveragedistributionNODE_702,9362468.04.00.6%Genus species strain EcoliAnna.
coveragedistributionNODE_712,870201.13.40.0%Genus species strain EcoliAnna.
coveragedistributionNODE_722,572268.61.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_732,343267.92.10.0%Genus species strain EcoliAnna.
coveragedistributionNODE_742,071422.75.00.1%Genus species strain EcoliAnna.
coveragedistributionNODE_751,794247.73.50.0%Genus species strain EcoliAnna.
coveragedistributionNODE_761,792228.34.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_771,765324.81.40.0%Genus species strain EcoliAnna.
coveragedistributionNODE_781,7022396.878.80.3%Genus species strain EcoliAnna.
coveragedistributionNODE_791,696382.110.30.0%Genus species strain EcoliAnna.
coveragedistributionNODE_801,345792.42.20.1%Genus species strain EcoliAnna.
coveragedistributionNODE_811,2551040.42.80.1%Genus species strain EcoliAnna.
coveragedistributionNODE_821,133456.512.30.0%Genus species strain EcoliAnna.
coveragedistributionNODE_831,1243890.97.30.3%Genus species strain EcoliAnna.
coveragedistributionNODE_841,117731.03.90.1%Genus species strain EcoliAnna.
coveragedistributionNODE_851,048240.25.50.0%Genus species strain EcoliAnna.
coveragedistributionNODE_861,031626.31.00.0%Genus species strain EcoliAnna.
coveragedistributionNODE_87970152.07.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_88848369.71.70.0%Genus species strain EcoliAnna.
coveragedistributionNODE_89813788.17.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_90734[583.7][60.0]0.0%Genus species strain EcoliAnna.
coveragedistributionNODE_917061923.01.30.1%Genus species strain EcoliAnna.
coveragedistributionNODE_92680[625.8][83.3]0.0%Genus species strain EcoliAnna.
coveragedistributionNODE_936671088.547.30.0%Genus species strain EcoliAnna.
coveragedistributionNODE_94576[1799.5][37.6]0.1%Genus species strain EcoliAnna.
coveragedistributionNODE_955661148.61.30.0%Genus species strain EcoliAnna.
coveragedistributionNODE_96556446.01.60.0%Genus species strain EcoliAnna.
coveragedistributionNODE_97556198.32.20.0%Genus species strain EcoliAnna.
coveragedistributionNODE_98531402.71.80.0%Genus species strain EcoliAnna.
coveragedistributionNODE_99417[157.4][34.9]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≤ 10000042132
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 ≤ 50001228
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.083

Junction Skew Score Calculation

reference sequencepr(no read start)
NODE_10.53696
NODE_20.51653
NODE_30.48692
NODE_40.52855
NODE_50.41718
NODE_60.44266
NODE_70.35075
NODE_80.49291
NODE_90.44718
NODE_100.42963
NODE_110.47839
NODE_120.42791
NODE_130.50963
NODE_140.39794
NODE_150.39720
NODE_160.54155
NODE_170.41469
NODE_180.45094
NODE_190.51054
NODE_200.50159
NODE_210.49060
NODE_220.40059
NODE_230.57237
NODE_240.38758
NODE_250.18409
NODE_260.45722
NODE_270.36200
NODE_280.37478
NODE_290.44573
NODE_300.47223
NODE_310.52088
NODE_320.45109
NODE_330.39889
NODE_340.37607
NODE_350.45076
NODE_360.47289
NODE_370.56565
NODE_380.39608
NODE_390.53045
NODE_400.40882
NODE_410.50021
NODE_420.55835
NODE_430.55029
NODE_440.51341
NODE_450.40503
NODE_460.39598
NODE_470.47513
NODE_480.37797
NODE_490.40914
NODE_500.55104
NODE_510.44072
NODE_520.47672
NODE_530.18646
NODE_540.55408
NODE_550.52793
NODE_560.34862
NODE_570.39145
NODE_580.49770
NODE_590.46958
NODE_600.40165
NODE_610.19557
NODE_620.52589
NODE_630.46375
NODE_640.44725
NODE_650.39934
NODE_660.48464
NODE_670.51902
NODE_680.43519
NODE_690.49043
NODE_700.05194
NODE_710.52398
NODE_720.47784
NODE_730.48058
NODE_740.33897
NODE_750.54400
NODE_760.52372
NODE_770.43003
NODE_780.09195
NODE_790.34855
NODE_800.20669
NODE_810.18247
NODE_820.35746
NODE_830.16586
NODE_840.22695
NODE_850.55487
NODE_860.29583
NODE_870.67010
NODE_880.45342
NODE_890.28659
NODE_90NA
NODE_910.20397
NODE_92NA
NODE_930.29910
NODE_94NA
NODE_950.28445
NODE_960.56433
NODE_970.72953
NODE_980.49153
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 input13:46:03 05 Mar 202013:48:16 05 Mar 20202 minutes 13 seconds
Read alignment to reference genome13:48:16 05 Mar 202013:51:55 05 Mar 20203 minutes 39 seconds
Preprocessing alignments for candidate junction identification13:51:55 05 Mar 202013:53:47 05 Mar 20201 minute 52 seconds
Preliminary analysis of coverage distribution13:53:47 05 Mar 202014:01:39 05 Mar 20207 minutes 52 seconds
Identifying junction candidates14:01:39 05 Mar 202014:15:47 05 Mar 202014 minutes 8 seconds
Re-alignment to junction candidates14:15:47 05 Mar 202014:16:50 05 Mar 20201 minute 3 seconds
Resolving best read alignments14:16:50 05 Mar 202014:19:56 05 Mar 20203 minutes 6 seconds
Creating BAM files14:19:56 05 Mar 202014:24:10 05 Mar 20204 minutes 14 seconds
Tabulating error counts14:24:10 05 Mar 202014:26:22 05 Mar 20202 minutes 12 seconds
Re-calibrating base error rates14:26:22 05 Mar 202014:27:56 05 Mar 20201 minute 34 seconds
Examining read alignment evidence14:27:56 05 Mar 202014:53:36 05 Mar 202025 minutes 40 seconds
Polymorphism statistics14:53:36 05 Mar 202014:53:38 05 Mar 20202 seconds
Output14:53:38 05 Mar 202014:55:55 05 Mar 20202 minutes 17 seconds
Total 1 hour 9 minutes 52 seconds