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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR22894676_R1.good.fq3,549,622455,739,766100.0%128.4 bases135 bases99.5%
errorsSRR22894676_R2.good.fq3,549,622455,731,019100.0%128.4 bases135 bases99.0%
total7,099,244911,470,785100.0%128.4 bases135 bases99.3%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionAssemblyC74_contig_1443,529403.18.019.8%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_2385,573353.19.315.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_3255,127278.45.67.8%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_4189,292268.75.55.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_5185,954375.87.07.7%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_6168,934321.57.36.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_7152,772390.66.96.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_8115,683358.07.34.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_9104,617292.86.23.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1098,564287.85.93.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1178,787362.97.43.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1259,337393.36.12.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1346,240286.05.41.5%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1441,348284.16.31.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1536,007269.75.51.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1635,103309.45.51.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1732,032381.27.01.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1827,075390.46.41.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_1919,031299.25.90.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_2015,862377.95.50.6%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_2110,843292.67.00.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_229,537257.55.70.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_239,396296.15.40.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_248,654363.58.40.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_258,555302.35.30.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_267,770351.05.80.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_277,728259.26.30.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_285,975278.17.90.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_294,892329.27.80.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_304,279230.37.30.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_313,3962318.027.10.8%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_323,311272.35.90.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_333,075671.310.60.2%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_342,107268.93.70.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_352,041217.25.20.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_361,754265.42.40.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_371,750571.911.40.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_381,652601.629.70.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_391,6432419.038.10.4%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_401,604308.04.60.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_411,330500.64.50.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_421,2432629.143.80.3%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_431,217294.14.20.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_441,136590.94.90.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_451,0021492.526.80.1%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_46883296.224.30.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_47882311.51.90.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_48844293.93.40.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_49764639.49.80.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_50745595.110.10.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_51723316.77.10.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_52702546.07.30.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_53622448.611.00.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_54611940.315.50.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_55585327.47.70.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_56494261.829.80.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_57493665.09.10.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_58462421.12.30.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_59453249.46.40.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_60439251.81.90.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_61423583.02.30.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_62391289.51.20.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_63383408.63.50.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_64352566.93.80.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_65349297.11.10.0%Enterococcus faecium AssemblyC74
coveragedistributionAssemblyC74_contig_66349278.91.20.0%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.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 10000027686
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 ≤ 5000628
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.066

Junction Skew Score Calculation

reference sequencepr(no read start)
AssemblyC74_contig_10.62866
AssemblyC74_contig_20.64701
AssemblyC74_contig_30.68081
AssemblyC74_contig_40.68723
AssemblyC74_contig_50.63859
AssemblyC74_contig_60.66022
AssemblyC74_contig_70.63014
AssemblyC74_contig_80.64585
AssemblyC74_contig_90.67692
AssemblyC74_contig_100.67631
AssemblyC74_contig_110.64526
AssemblyC74_contig_120.63132
AssemblyC74_contig_130.67606
AssemblyC74_contig_140.68059
AssemblyC74_contig_150.68693
AssemblyC74_contig_160.66511
AssemblyC74_contig_170.64060
AssemblyC74_contig_180.62841
AssemblyC74_contig_190.67503
AssemblyC74_contig_200.64116
AssemblyC74_contig_210.68334
AssemblyC74_contig_220.67604
AssemblyC74_contig_230.67999
AssemblyC74_contig_240.64876
AssemblyC74_contig_250.68165
AssemblyC74_contig_260.64723
AssemblyC74_contig_270.70484
AssemblyC74_contig_280.68311
AssemblyC74_contig_290.67263
AssemblyC74_contig_300.71908
AssemblyC74_contig_310.39311
AssemblyC74_contig_320.70734
AssemblyC74_contig_330.55398
AssemblyC74_contig_340.71310
AssemblyC74_contig_350.72650
AssemblyC74_contig_360.70729
AssemblyC74_contig_370.59677
AssemblyC74_contig_380.61199
AssemblyC74_contig_390.37219
AssemblyC74_contig_400.68363
AssemblyC74_contig_410.60376
AssemblyC74_contig_420.40628
AssemblyC74_contig_430.69253
AssemblyC74_contig_440.63155
AssemblyC74_contig_450.47255
AssemblyC74_contig_460.71291
AssemblyC74_contig_470.72727
AssemblyC74_contig_480.73874
AssemblyC74_contig_490.62958
AssemblyC74_contig_500.62685
AssemblyC74_contig_510.75577
AssemblyC74_contig_520.65670
AssemblyC74_contig_530.66720
AssemblyC74_contig_540.53663
AssemblyC74_contig_550.70410
AssemblyC74_contig_560.76721
AssemblyC74_contig_570.65822
AssemblyC74_contig_580.69057
AssemblyC74_contig_590.78366
AssemblyC74_contig_600.82045
AssemblyC74_contig_610.97761
AssemblyC74_contig_620.90370
AssemblyC74_contig_630.68536
AssemblyC74_contig_640.72275
AssemblyC74_contig_650.79897
AssemblyC74_contig_660.70745

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 input14:13:45 19 Apr 202314:15:59 19 Apr 20232 minutes 14 seconds
Read alignment to reference genome14:15:59 19 Apr 202314:30:14 19 Apr 202314 minutes 15 seconds
Preprocessing alignments for candidate junction identification14:30:14 19 Apr 202314:31:37 19 Apr 20231 minute 23 seconds
Preliminary analysis of coverage distribution14:31:37 19 Apr 202314:35:27 19 Apr 20233 minutes 50 seconds
Identifying junction candidates14:35:27 19 Apr 202314:36:31 19 Apr 20231 minute 4 seconds
Re-alignment to junction candidates14:36:31 19 Apr 202314:41:57 19 Apr 20235 minutes 26 seconds
Resolving best read alignments14:41:57 19 Apr 202314:44:23 19 Apr 20232 minutes 26 seconds
Creating BAM files14:44:23 19 Apr 202314:46:59 19 Apr 20232 minutes 36 seconds
Tabulating error counts14:46:59 19 Apr 202314:48:17 19 Apr 20231 minute 18 seconds
Re-calibrating base error rates14:48:17 19 Apr 202314:48:54 19 Apr 202337 seconds
Examining read alignment evidence14:48:54 19 Apr 202315:05:07 19 Apr 202316 minutes 13 seconds
Polymorphism statistics15:05:07 19 Apr 202315:05:08 19 Apr 20231 second
Output15:05:08 19 Apr 202315:05:51 19 Apr 202343 seconds
Total 52 minutes 6 seconds