breseq  version 0.24rc1  revision 83e50355436e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,351,1710T→G100.0% 4.9 6intergenic (+85/+144)yhdZ/rrfFpredicted amino‑acid transporter subunit/5S ribosomal RNA
*REL6061,602,1010C→T100.0% 2.1 3intergenic (+124/+104)pinQ/ECB_01505predicted site‑specific recombinase/conserved hypothetical protein
*REL6062,650,8330T→C100.0% 2.0 2intergenic (‑156/+29)rrlG/gltW23S ribosomal RNA/tRNA‑Glu
*REL6062,650,8340C→A100.0% 2.0 2intergenic (‑157/+28)rrlG/gltW23S ribosomal RNA/tRNA‑Glu
*REL606569,0340G→A100.0% 1.9 2903yhhIpredicted transposase
*REL606569,0360T→A100.0% 1.9 2901yhhIpredicted transposase
*REL6062,650,8370C→T100.0% 1.9 2intergenic (‑160/+25)rrlG/gltW23S ribosomal RNA/tRNA‑Glu
*REL6061,605,8590A→C100.0% 1.8 424stfRpredicted tail fiber protein
*REL6061,110,5990G→A100.0% 1.7 2777insF‑1putative transposase for IS3
*REL6062,650,8490A→T100.0% 1.7 2intergenic (‑172/+13)rrlG/gltW23S ribosomal RNA/tRNA‑Glu
*REL6062,650,8390A→G100.0% 1.5 2intergenic (‑162/+23)rrlG/gltW23S ribosomal RNA/tRNA‑Glu
*REL606569,2940A→T100.0% 1.4 2643yhhIpredicted transposase
*REL6062,842,1280C→G100.0% 1.4 3noncoding (13/77 nt)metWtRNA‑Met
*REL6063,354,7020G→T100.0% 1.4 2intergenic (‑23/+161)rrlD/alaU23S ribosomal RNA/tRNA‑Ala
*REL6061,110,6030C→T100.0% 1.1 2773insF‑1putative transposase for IS3
*REL6061,607,9460G→T100.0% 1.1 1intergenic (‑14/‑27)ECB_01510/insE‑3putative tail component of prophage/putative transposase‑related protein
*REL6061,545,1160G→T100.0% 1.0 2881gadBglutamate decarboxylase B, PLP‑dependent
*REL606573,2020T→G100.0% 0.9 8287ECB_00530conserved hypothetical protein
*REL6062,453,9780G→C100.0% 0.7 2noncoding (52/76 nt)valXtRNA‑Val
*REL6063,555,6880A→G100.0% 0.4 1623yhhIpredicted transposase
*REL606569,9160C→A100.0% 0.3 121yhhIpredicted transposase

Marginal mixed read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL60633,8010T→G29.4% 11.63480carAcarbamoyl‑phosphate synthase small subunit
*REL60687,8120T→G38.5% 21.752641leuOleucine transcriptional activator
*REL60692,3590G→T25.0% 14.040intergenic (+523/‑79)fruR/yabBDNA‑binding transcriptional dual regulator/hypothetical protein
*REL60693,9460G→C36.7% 19.050111ftsLmembrane bound cell division protein at septum containing leucine zipper motif
*REL606100,4080T→G29.0% 11.263518murDUDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑ glutamatesynthetase
*REL606139,8120G→T36.4% 26.044intergenic (‑92/‑74)yacC/cueOhypothetical protein/multicopper oxidase (laccase)
*REL606157,9940G→T25.7% 10.335277htrEpredicted outer membrane usher protein
*REL606165,6690T→G29.8% 12.147714hrpBpredicted ATP‑dependent helicase
*REL606260,1810T→G28.1% 12.06427pepDaminoacyl‑histidine dipeptidase (peptidase D)
*REL606260,1840A→G32.2% 22.15924pepDaminoacyl‑histidine dipeptidase (peptidase D)
*REL606398,4450T→G16.7% 10.148518secFprotein export protein SecF
*REL606402,0560T→G33.3% 12.566180ribDfused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
*REL606506,2070T→G25.0% 11.868126gclglyoxylate carboligase
*REL606583,8050A→C32.5% 12.641944phePphenylalanine transporter
*REL606642,5170T→G25.0% 10.556283lipAlipoyl synthase
*REL606676,2630T→G24.7% 13.073788yleAisopentenyl‑adenosine A37 tRNA methylthiolase
*REL606869,8210A→G30.4% 11.556767yliGpredicted SAM‑dependent methyltransferase
*REL606964,8050A→G27.4% 14.963484ycaMpredicted transporter
*REL606986,0540T→G33.3% 10.431597lpxKtetraacyldisaccharide 4'‑kinase
*REL606987,4560G→T24.5% 12.249976ycaQhypothetical protein
*REL6061,029,2410T→C20.7% 11.558150pqiAparaquat‑inducible membrane protein A
*REL6061,029,2450A→C32.1% 13.857154pqiAparaquat‑inducible membrane protein A
*REL6061,117,1810G→T30.8% 11.940585csgDDNA‑binding transcriptional activator in two‑component regulatory system
*REL6061,168,1360C→G27.8% 10.536268pabC4‑amino‑4‑deoxychorismate lyase
*REL6061,242,9060T→G27.9% 10.861325ldcAL,D‑carboxypeptidase A
*REL6061,318,1080T→G37.5% 10.224871trpDbifunctional indole‑3‑glycerol‑phosphate synthase/anthranilate phosphoribosyltransferase
*REL6061,509,9360A→G40.0% 18.940pseudogene (74/567 nt)yddEhypothetical protein; b1464_2
*REL6061,536,7740G→T28.8% 16.560241ddpXD‑ala‑D‑ala dipeptidase, Zn‑dependent
*REL6061,538,2350G→T25.9% 11.9541437doscAMP phosphodiesterase, heme‑regulated
*REL6061,595,1110T→G25.4% 18.25536dcpdipeptidyl carboxypeptidase II
*REL6061,714,6340T→A19.5% 13.142intergenic (‑77/+89)ydhP/ECB_01628putative transport protein (MFS family); b1657_2/predicted transporter
*REL6061,714,6400T→A17.5% 10.643intergenic (‑83/+83)ydhP/ECB_01628putative transport protein (MFS family); b1657_2/predicted transporter
*REL6061,812,7200G→T33.3% 11.127685ydjZconserved inner membrane protein
*REL6061,854,3850C→G34.9% 19.643248yeaOhypothetical protein
*REL6061,854,3880A→G33.3% 12.339251yeaOhypothetical protein
*REL6062,006,2940A→C23.3% 13.960365insDIS2 insertion element transposase InsAB'
*REL6062,056,8490T→G28.6% 10.949877cpsBmannose‑1‑phosphate guanyltransferase
*REL6062,167,5690T→G35.7% 10.943105yehWpredicted transporter subunit: membrane component of ABC superfamily
*REL6062,197,8670T→G28.3% 11.460141cirAferric iron‑catecholate outer membrane transporter
*REL6062,233,5190T→G31.5% 10.6561700yejHpredicted ATP‑dependet helicase
*REL6062,304,3690A→G29.5% 11.561758yfaDhypothetical protein
*REL6062,402,8890T→C33.3% 12.0391245yfcYacetyl‑CoA acetyltransferase
*REL6062,433,4540A→T19.7% 13.261559ypdApredicted sensory kinase in two‑component system with YpdB
*REL6062,501,9620T→G25.0% 11.2401499tktBtransketolase 2, thiamin‑binding
*REL6062,698,0930T→.66.7% 54.336coding (1994/2145 nt)nrdEribonucleotide‑diphosphate reductase alpha subunit
*REL6063,000,2400C→G20.8% 12.048677fluantigen 43 (Ag43) phase‑variable biofilm formation autotransporter
*REL6063,037,5980A→C31.6% 10.5381397ECB_02838GspD, hypothetical type II secretion protein
*REL6063,176,1310T→C28.8% 11.052218uxaAaltronate hydrolase
*REL6063,218,9620A→G27.9% 10.543587agaYtagatose 6‑phosphate aldolase 1, kbaY subunit
*REL6063,268,9910T→G28.2% 18.43948ispBoctaprenyl diphosphate synthase
*REL6063,279,7860T→G31.4% 10.153608yhbGpredicted transporter subunit: ATP‑binding component of ABC superfamily
*REL6063,289,1960A→C32.4% 13.03790yhcCpredicted Fe‑S oxidoreductase
*REL6063,356,9990G→T31.6% 78.5165intergenic (‑332/‑142)rrsD/yrdA16S ribosomal RNA/hypothetical protein
*REL6063,357,0000A→T56.1% 104.3163intergenic (‑333/‑141)rrsD/yrdA16S ribosomal RNA/hypothetical protein
*REL6063,357,0020C→T49.0% 161.6162intergenic (‑335/‑139)rrsD/yrdA16S ribosomal RNA/hypothetical protein
*REL6063,357,0100C→T53.5% 117.6161intergenic (‑343/‑131)rrsD/yrdA16S ribosomal RNA/hypothetical protein
*REL6063,357,0120G→T62.3% 81.0151intergenic (‑345/‑129)rrsD/yrdA16S ribosomal RNA/hypothetical protein
*REL6063,357,0160G→T63.3% 94.6146intergenic (‑349/‑125)rrsD/yrdA16S ribosomal RNA/hypothetical protein
*REL6063,357,0190G→T65.7% 92.2154intergenic (‑352/‑122)rrsD/yrdA16S ribosomal RNA/hypothetical protein
*REL6063,361,4730T→C26.0% 11.650intergenic (‑8/‑122)smf/defhypothetical protein/peptide deformylase
*REL6063,369,8680T→G26.7% 10.430136rpsK30S ribosomal protein S11
*REL6063,424,8620A→T30.9% 20.744intergenic (+80/‑46)nirD/nirCnitrite reductase small subunit/nitrite transporter
*REL6063,424,8630A→T27.9% 13.244intergenic (+81/‑45)nirD/nirCnitrite reductase small subunit/nitrite transporter
*REL6063,424,8700G→T25.0% 11.441intergenic (+88/‑38)nirD/nirCnitrite reductase small subunit/nitrite transporter
*REL6063,424,8750A→T27.5% 18.445intergenic (+93/‑33)nirD/nirCnitrite reductase small subunit/nitrite transporter
*REL6063,424,8820G→T29.2% 23.949intergenic (+100/‑26)nirD/nirCnitrite reductase small subunit/nitrite transporter
*REL6063,450,8720A→C23.8% 11.342562yrfDpredicted pilus assembly protein
*REL6063,535,0350T→C26.9% 11.152intergenic (‑104/‑46)ftsY/yhhFfused Signal Recognition Particle (SRP) receptor: membrane binding protein/conserved protein/predicted methyltransferase
*REL6063,560,6960G→T18.6% 11.961595yhiIpredicted HlyD family secretion protein
*REL6063,577,4110T→G32.3% 13.331423gorglutathione reductase
*REL6063,610,8600A→G17.9% 10.478573yhjJpredicted zinc‑dependent peptidase
*REL6063,671,9740C→A23.6% 18.45565yiaIpredicted hydrogenase, 4Fe‑4S ferredoxin‑type component
*REL6063,758,6260A→C32.6% 15.043902yicFNAD‑dependent DNA ligase LigB
*REL6063,781,6570G→T31.1% 15.045322ECB_03521conserved hypothetical protein
*REL6063,977,9930A→G27.1% 15.760514metE5‑methyltetrahydropteroyltriglutamate‑ homocysteine methyltransferase
*REL6064,080,9860T→G41.7% 10.325intergenic (+74/‑186)sodA/kdgTsuperoxide dismutase, Mn/2‑keto‑3‑deoxygluconate permease
*REL6064,126,0830T→G21.4% 12.7581982pflDpredicted formate acetyltransferase 2 (pyruvate formate lyase II)
*REL6064,320,3820A→G33.3% 11.036intergenic (‑40/‑243)melR/melADNA‑binding transcriptional dual regulator/alpha‑galactosidase, NAD(P)‑binding
*REL6064,462,9910A→T61.1% 119.0207229yjgNconserved inner membrane protein
*REL6064,462,9920G→T33.0% 133.5209230yjgNconserved inner membrane protein
*REL6064,462,9950G→T42.1% 163.9212233yjgNconserved inner membrane protein
*REL6064,462,9970C→T54.0% 171.4214235yjgNconserved inner membrane protein
*REL6064,463,0000G→T42.0% 175.0198238yjgNconserved inner membrane protein
*REL6064,463,0060G→T51.7% 204.0198244yjgNconserved inner membrane protein
*REL6064,463,0140C→T38.4% 104.0130252yjgNconserved inner membrane protein
*REL6064,463,0160A→T49.1% 144.4116254yjgNconserved inner membrane protein
*REL6064,488,1000G→T28.0% 12.751922yjhCpredicted oxidoreductase
*REL6064,520,3730G→T29.6% 11.054intergenic (‑734/‑722)yjhA/fimBN‑acetylnuraminic acid outer membrane channel protein/recombinase involved in phase variation; regulator for fimA; b4312_1
*REL6064,582,4710T→G36.4% 12.9341580tsrmethyl‑accepting chemotaxis protein I, serine sensor receptor
*REL6064,620,0030C→G22.2% 12.4451058sltlytic murein transglycosylase, soluble
*REL6064,621,2740A→G26.0% 15.850302trpRTrp operon repressor
*REL6064,628,0270T→G25.9% 11.358440arcADNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA

Marginal new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 809428 =43 (0.910)8 (0.170) 6/60 4.4 16.0% intergenic (‑155/‑242) ybhK/moaA predicted transferase with NAD(P)‑binding Rossmann‑fold domain/molybdenum cofactor biosynthesis protein A
?REL606 = 4141016 41 (0.740)coding (89/705 nt) yijC DNA‑binding transcriptional repressor
* ? REL606 1427340 =46 (0.890)6 (0.120) 4/66 5.7 13.2% intergenic (‑115/+26) ynaF/ompN stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
?REL606 4022380 = 33 (0.600)intergenic (+39/‑116) dsbA/yihF periplasmic protein disulfide isomerase I/hypothetical protein
* ? REL606 = 374957240 (0.880)8 (0.180) 4/58 5.2 16.5% intergenic (‑65/+33) mutM/rpmG formamidopyrimidine‑DNA glycosylase/50S ribosomal protein L33
?REL606 = 4157631 41 (0.740)coding (278/546 nt) nusG transcription antitermination protein NusG
* ? REL606 = 381306239 (0.850)8 (0.180) 4/58 5.2 16.7% intergenic (‑143/‑791) ivbL/emrD ilvB operon leader peptide/multidrug efflux system protein
?REL606 = 4157631 41 (0.740)coding (278/546 nt) nusG transcription antitermination protein NusG
* ? REL606 3944627 =36 (0.820)8 (0.180) 4/56 5.1 17.0% intergenic (+16/‑131) proM/aslB tRNA‑Pro/predicted regulator of arylsulfatase activity
?REL606 = 4157630 42 (0.760)coding (277/546 nt) nusG transcription antitermination protein NusG
* ? REL606 72407 =27 (0.610)4 (0.090) 4/56 5.1 9.1% coding (446/1701 nt) araB ribulokinase
?REL606 3650765 = 53 (0.960)intergenic (+46/+141) cspA/hokA major cold shock protein/toxic polypeptide, small
* ? REL606 = 144001848 (1.170)3 (0.070) 3/52 5.3 5.9% coding (894/1500 nt) feaB phenylacetaldehyde dehydrogenase
?REL606 = 4081044 47 (0.850)intergenic (+132/‑128) sodA/kdgT superoxide dismutase, Mn/2‑keto‑3‑deoxygluconate permease
* ? REL606 2429311 =33 (0.780)4 (0.090) 3/54 5.5 11.0% coding (206/243 nt) yfdY predicted inner membrane protein
?REL606 = 2792989 32 (0.580)coding (481/849 nt) ECB_02621 conserved hypothetical protein