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

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsSRR22894678_R1.good.fq2,458,357318,785,675100.0%129.7 bases136 bases99.5%
errorsSRR22894678_R2.good.fq2,458,357318,781,307100.0%129.7 bases136 bases98.9%
total4,916,714637,566,982100.0%129.7 bases136 bases99.2%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionTrimmedAssembly_T66_contig_1655,835147.73.515.5%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_2291,973237.54.011.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_3262,583230.44.19.6%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_4245,870202.33.67.9%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_5187,153202.43.76.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_6156,776186.53.44.6%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_7138,687158.83.53.5%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_8137,664169.93.23.7%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_9133,707214.93.64.6%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1098,898173.23.42.7%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1196,142178.43.32.7%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1294,931163.63.52.5%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1394,334224.83.63.4%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1491,033211.93.93.1%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1590,630218.94.03.2%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1689,249187.23.02.7%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1766,738166.12.71.8%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1853,854181.13.61.5%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_1946,603220.74.21.6%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_2039,141167.43.51.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_2129,409310.96.11.4%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_2225,952208.15.10.8%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_2324,421206.43.81.2%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_2419,315219.03.80.7%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_255,544209.33.80.2%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_263,462180.03.20.1%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_273,273206.53.50.1%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_283,1831004.313.70.5%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_292,480168.82.70.1%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_302,0235268.952.41.6%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_311,737169.91.60.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_321,640963.813.80.2%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_331,499184.63.20.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_341,203384.06.40.1%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_351,096384.75.90.1%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_368641470.78.60.2%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_37853434.49.50.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_387571447.150.10.1%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_39663221.03.50.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_40631198.22.40.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_41437465.49.90.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
coveragedistributionTrimmedAssembly_T66_contig_423201257.024.90.0%Lactiplantibacillus plantarum Lactobacillus plantarum_DTU
total3,202,563100.0%

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≤ 10000010005
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 ≤ 5000145
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.012

Junction Skew Score Calculation

reference sequencepr(no read start)
TrimmedAssembly_T66_contig_10.76925
TrimmedAssembly_T66_contig_20.70673
TrimmedAssembly_T66_contig_30.71078
TrimmedAssembly_T66_contig_40.72794
TrimmedAssembly_T66_contig_50.72773
TrimmedAssembly_T66_contig_60.73847
TrimmedAssembly_T66_contig_70.75970
TrimmedAssembly_T66_contig_80.75029
TrimmedAssembly_T66_contig_90.71810
TrimmedAssembly_T66_contig_100.74993
TrimmedAssembly_T66_contig_110.74349
TrimmedAssembly_T66_contig_120.75819
TrimmedAssembly_T66_contig_130.71342
TrimmedAssembly_T66_contig_140.72321
TrimmedAssembly_T66_contig_150.71784
TrimmedAssembly_T66_contig_160.73863
TrimmedAssembly_T66_contig_170.75412
TrimmedAssembly_T66_contig_180.74292
TrimmedAssembly_T66_contig_190.71716
TrimmedAssembly_T66_contig_200.75043
TrimmedAssembly_T66_contig_210.67118
TrimmedAssembly_T66_contig_220.72785
TrimmedAssembly_T66_contig_230.68854
TrimmedAssembly_T66_contig_240.71916
TrimmedAssembly_T66_contig_250.72965
TrimmedAssembly_T66_contig_260.75422
TrimmedAssembly_T66_contig_270.74269
TrimmedAssembly_T66_contig_280.52655
TrimmedAssembly_T66_contig_290.77871
TrimmedAssembly_T66_contig_300.32823
TrimmedAssembly_T66_contig_310.77438
TrimmedAssembly_T66_contig_320.51463
TrimmedAssembly_T66_contig_330.76785
TrimmedAssembly_T66_contig_340.67456
TrimmedAssembly_T66_contig_350.68704
TrimmedAssembly_T66_contig_360.56704
TrimmedAssembly_T66_contig_370.67175
TrimmedAssembly_T66_contig_380.53104
TrimmedAssembly_T66_contig_390.74684
TrimmedAssembly_T66_contig_400.76673
TrimmedAssembly_T66_contig_410.72998
TrimmedAssembly_T66_contig_420.63906

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 input14:09:03 19 Apr 202314:10:44 19 Apr 20231 minute 41 seconds
Read alignment to reference genome14:10:44 19 Apr 202314:21:46 19 Apr 202311 minutes 2 seconds
Preprocessing alignments for candidate junction identification14:21:46 19 Apr 202314:22:44 19 Apr 202358 seconds
Preliminary analysis of coverage distribution14:22:44 19 Apr 202314:25:07 19 Apr 20232 minutes 23 seconds
Identifying junction candidates14:25:07 19 Apr 202314:25:13 19 Apr 20236 seconds
Re-alignment to junction candidates14:25:13 19 Apr 202314:27:46 19 Apr 20232 minutes 33 seconds
Resolving best read alignments14:27:46 19 Apr 202314:29:18 19 Apr 20231 minute 32 seconds
Creating BAM files14:29:18 19 Apr 202314:31:03 19 Apr 20231 minute 45 seconds
Tabulating error counts14:31:03 19 Apr 202314:31:56 19 Apr 202353 seconds
Re-calibrating base error rates14:31:56 19 Apr 202314:32:14 19 Apr 202318 seconds
Examining read alignment evidence14:32:14 19 Apr 202314:43:31 19 Apr 202311 minutes 17 seconds
Polymorphism statistics14:43:31 19 Apr 202314:43:32 19 Apr 20231 second
Output14:43:32 19 Apr 202314:44:02 19 Apr 202330 seconds
Total 34 minutes 59 seconds