breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR22894674_R1.good.fq2,924,254375,960,437100.0%128.6 bases135 bases99.5%
errorsSRR22894674_R2.good.fq2,924,254375,948,641100.0%128.6 bases135 bases99.0%
total5,848,508751,909,078100.0%128.6 bases135 bases99.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAssemblyC74_contig_1443,529314.54.818.8%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_2385,573280.45.014.5%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_3255,127236.73.98.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_4189,292244.84.06.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_5185,954297.14.77.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_6168,934267.74.26.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_7152,772321.24.86.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_8115,683282.64.44.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_9104,617250.04.33.5%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1098,564240.24.13.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1178,787294.24.43.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1259,337314.14.32.5%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1346,240248.13.91.5%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1441,348249.94.11.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1536,007307.04.61.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1635,103259.84.01.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1732,032294.44.61.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1827,075310.94.51.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1919,031262.34.50.7%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_2015,862291.44.70.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_2110,843255.13.30.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_229,537284.04.70.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_239,396247.34.30.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_248,654309.65.80.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_258,555257.64.90.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_267,770299.74.80.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_277,728294.05.00.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_285,975308.46.30.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_294,892272.65.60.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_304,279280.15.60.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_313,3961872.718.30.8%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_323,311310.37.60.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_333,075523.57.80.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_342,107231.53.10.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_352,041262.87.20.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_361,754309.64.50.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_371,750659.011.30.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_381,652499.511.20.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_391,6431922.932.40.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_401,604249.84.20.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_411,330574.94.90.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_421,2432525.029.10.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_431,217327.73.00.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_441,136635.79.50.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_451,0021326.914.30.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_46883231.84.20.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_47882328.45.10.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_48844326.72.90.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_49764546.56.30.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_50745505.85.10.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_51723324.82.50.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_52702538.85.30.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_53622540.14.40.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_54611706.86.60.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_55585262.33.60.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_56494271.96.20.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_57493538.55.70.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_58462327.82.80.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_59453174.09.50.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_60439295.51.00.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_61423633.25.80.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_62391311.91.20.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_63383337.31.60.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_64352620.312.00.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_65349[315.3][17.0]0.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_66349300.82.70.0%Enterococcus faecium AssemblyC74
total2,608,706100.0%

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≤ 10000026417
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000691
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.073

Junction Skew Score Calculation

reference sequencepr(no read start)
AssemblyC74_contig_10.66809
AssemblyC74_contig_20.68323
AssemblyC74_contig_30.70781
AssemblyC74_contig_40.70294
AssemblyC74_contig_50.67563
AssemblyC74_contig_60.69059
AssemblyC74_contig_70.66370
AssemblyC74_contig_80.68564
AssemblyC74_contig_90.70292
AssemblyC74_contig_100.70417
AssemblyC74_contig_110.67976
AssemblyC74_contig_120.66712
AssemblyC74_contig_130.70304
AssemblyC74_contig_140.70367
AssemblyC74_contig_150.67374
AssemblyC74_contig_160.69312
AssemblyC74_contig_170.68330
AssemblyC74_contig_180.66928
AssemblyC74_contig_190.69542
AssemblyC74_contig_200.67978
AssemblyC74_contig_210.70488
AssemblyC74_contig_220.68087
AssemblyC74_contig_230.70634
AssemblyC74_contig_240.67554
AssemblyC74_contig_250.70649
AssemblyC74_contig_260.67375
AssemblyC74_contig_270.68976
AssemblyC74_contig_280.67164
AssemblyC74_contig_290.69627
AssemblyC74_contig_300.70243
AssemblyC74_contig_310.42270
AssemblyC74_contig_320.68864
AssemblyC74_contig_330.60764
AssemblyC74_contig_340.73469
AssemblyC74_contig_350.70076
AssemblyC74_contig_360.67729
AssemblyC74_contig_370.58398
AssemblyC74_contig_380.64588
AssemblyC74_contig_390.40018
AssemblyC74_contig_400.70421
AssemblyC74_contig_410.59474
AssemblyC74_contig_420.40587
AssemblyC74_contig_430.68356
AssemblyC74_contig_440.62058
AssemblyC74_contig_450.47904
AssemblyC74_contig_460.74462
AssemblyC74_contig_470.72118
AssemblyC74_contig_480.72097
AssemblyC74_contig_490.63874
AssemblyC74_contig_500.65705
AssemblyC74_contig_510.72156
AssemblyC74_contig_520.65242
AssemblyC74_contig_530.64469
AssemblyC74_contig_540.58054
AssemblyC74_contig_550.73810
AssemblyC74_contig_560.76012
AssemblyC74_contig_570.68458
AssemblyC74_contig_580.73780
AssemblyC74_contig_590.79691
AssemblyC74_contig_600.80208
AssemblyC74_contig_610.92000
AssemblyC74_contig_620.91791
AssemblyC74_contig_630.72674
AssemblyC74_contig_640.64596
AssemblyC74_contig_65NA
AssemblyC74_contig_660.71429

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 cutoff0.75
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
bowtie22.2.6
R3.4.4

Execution Times

stepstartendelapsed
Read and reference sequence file input14:10:48 19 Apr 202314:12:40 19 Apr 20231 minute 52 seconds
Read alignment to reference genome14:12:40 19 Apr 202314:26:45 19 Apr 202314 minutes 5 seconds
Preprocessing alignments for candidate junction identification14:26:45 19 Apr 202314:27:52 19 Apr 20231 minute 7 seconds
Preliminary analysis of coverage distribution14:27:52 19 Apr 202314:31:19 19 Apr 20233 minutes 27 seconds
Identifying junction candidates14:31:19 19 Apr 202314:32:38 19 Apr 20231 minute 19 seconds
Re-alignment to junction candidates14:32:38 19 Apr 202314:37:36 19 Apr 20234 minutes 58 seconds
Resolving best read alignments14:37:36 19 Apr 202314:39:35 19 Apr 20231 minute 59 seconds
Creating BAM files14:39:35 19 Apr 202314:41:45 19 Apr 20232 minutes 10 seconds
Tabulating error counts14:41:45 19 Apr 202314:42:48 19 Apr 20231 minute 3 seconds
Re-calibrating base error rates14:42:48 19 Apr 202314:43:24 19 Apr 202336 seconds
Examining read alignment evidence14:43:24 19 Apr 202314:56:46 19 Apr 202313 minutes 22 seconds
Polymorphism statistics14:56:46 19 Apr 202314:56:47 19 Apr 20231 second
Output14:56:47 19 Apr 202314:57:30 19 Apr 202343 seconds
Total 46 minutes 42 seconds