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

Predicted mutation
evidence position mutation annotation gene description
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 29220 29252 33 2 [1] [1] 4 dapB/carA 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
* * ÷ NZ_CP009273 80514 80580 67 2 [1] [1] 2 leuL/leuO leu operon leader peptide/transcriptional regulator LeuO
* * ÷ NZ_CP009273 81904 81931 28 2 [1] [1] 3 leuO/BW25113_RS25405 transcriptional regulator LeuO/protein YabR
* * ÷ NZ_CP009273 118328 118338 11 3 [1] [0] 2 aroP/pdhR aromatic amino acid transporter AroP/pyruvate dehydrogenase complex transcriptional repressor PdhR
* * ÷ NZ_CP009273 153637 153645 9 2 [0] [1] 3 yadN/folK fimbrial protein/2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine diphosphokinase
* * ÷ NZ_CP009273 233688 233750 63 2 [0] [1] 2 BW25113_RS01085/BW25113_RS01090 tRNA‑Asp/lipoprotein
* * ÷ NZ_CP009273 235007 235122 116 3 [1] [0] 2 BW25113_RS01095 hypothetical protein
* * ÷ NZ_CP009273 255904 255955 52 2 [1] [1] 2 phoE/proB phosphoporin PhoE/glutamate 5‑kinase
* * ÷ NZ_CP009273 280871 280975 105 2 [0] [1] 2 [yagF] [yagF]
* * ÷ NZ_CP009273 356978 357568 591 4 [1] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 385318 385407 90 3 [1] [1] 3 hemB/BW25113_RS01915 porphobilinogen synthase/outer membrane autotransporter barrel domain‑containing protein
* * ÷ NZ_CP009273 396647 396709 63 2 [1] [1] 3 [BW25113_RS25915] [BW25113_RS25915]
* * ÷ NZ_CP009273 518580 518609 30 2 [1] [1] 2 ybbP/rhsD ABC transporter permease/rhs element protein RhsD
* * ÷ NZ_CP009273 524116 524232 117 2 [0] [1] 3 BW25113_RS24960 hypothetical protein
* * ÷ NZ_CP009273 564260 564316 57 2 [1] [0] 2 [BW25113_RS25485] [BW25113_RS25485]
* * ÷ NZ_CP009273 578977 579078 102 3 [1] [1] 3 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 647495 647583 89 3 [1] [1] 2 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 651724 651732 9 4 [0] [1] 3 dcuC/pagP anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP
* * ÷ NZ_CP009273 656861 656895 35 2 [1] [1] 3 ybeF/lipB YbeF family transcriptional regulator/lipoyl(octanoyl) transferase LipB
* * ÷ NZ_CP009273 716369 716481 113 2 [1] [0] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 724885 724896 12 3 [1] [1] 2 ybfA/rhsC YbfA family protein/rhs element protein RhsC
* * ÷ NZ_CP009273 748526 748538 13 2 [0] [0] 3 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 761148 761158 11 2 [1] [0] 2 mngR mannosyl‑D‑glycerate transport/metabolism system transcriptional repressor MngR
* * ÷ NZ_CP009273 761386 761407 22 2 [1] [1] 2 mngR/mngA mannosyl‑D‑glycerate transport/metabolism system transcriptional repressor MngR/PTS 2‑O‑a‑mannosyl‑D‑glycerate transporter subunit IIABC
* * ÷ NZ_CP009273 766544 766554 11 2 [0] [0] 2 mngB/cydA mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
* * ÷ NZ_CP009273 982718 982736 19 2 [0] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 993197 993278 82 2 [0] [1] 4 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1028369 1028400 32 2 [1] [1] 2 hyaA hydrogenase 1 small subunit
* * ÷ NZ_CP009273 1098944 1098980 37 2 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1103885 1103927 43 2 [1] [1] 2 mdoC glucans biosynthesis protein MdoC
* * ÷ NZ_CP009273 1114571 1114640 70 2 [1] [1] 3 yceJ/BW25113_RS05515 cytochrome b/YceO family protein
* * ÷ NZ_CP009273 1193088 1193094 7 4 [0] [1] 3 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1205761 1205828 68 2 [0] [1] 3 [mcrA] [mcrA]
* * ÷ NZ_CP009273 1207491 1207622 132 3 [1] [1] 5 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1251678 1251683 6 2 [0] [0] 2 ycgV/ychF autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF
* * ÷ NZ_CP009273 1274916 1274943 28 6 [1] [0] 5 narK/narG nitrate transporter NarK/nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1320828 1320881 54 2 [1] [1] 3 yciQ DUF2207 domain‑containing protein
* * ÷ NZ_CP009273 1389950 1390015 66 3 [1] [1] 2 ynaI low conductance mechanosensitive channel YnaI
* * ÷ NZ_CP009273 1459356 1459470 115 2 [1] [0] 2 [BW25113_RS25580] [BW25113_RS25580]
* * ÷ NZ_CP009273 1459506 1459534 29 2 [0] [1] 2 BW25113_RS25580/BW25113_RS07350 hypothetical protein/autotransporter domain‑containing protein
* * ÷ NZ_CP009273 1524310 1524430 121 2 [1] [1] 3 [BW25113_RS26145] [BW25113_RS26145]
* * ÷ NZ_CP009273 1539063 1539094 32 3 [1] [1] 3 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1540372 1540510 139 2 [1] [1] 3 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1577072 1577109 38 2 [0] [1] 2 ydeN/ydeO sulfatase/acid stress response transcriptional regulator YdeO
* * ÷ NZ_CP009273 1618916 1618970 55 3 [1] [1] 2 ydeI/ydeJ YdeI family stress tolerance OB fold protein/2‑oxo‑tetronate isomerase
* * ÷ NZ_CP009273 1631953 1632041 89 2 [0] [0] 2 [gnsB] [gnsB]
* * ÷ NZ_CP009273 1634988 1635037 50 2 [0] [1] 4 essD/ynfU phage lysis protein EssD/putative zinc‑binding protein YnfU
* * ÷ NZ_CP009273 1635248 1635285 38 2 [1] [0] 5 ynfU/cspB putative zinc‑binding protein YnfU/cold shock‑like protein CspB
* * ÷ NZ_CP009273 1744842 1744852 11 2 [0] [1] 8 ydhX 4Fe‑4S dicluster domain‑containing protein
* * ÷ NZ_CP009273 1748982 1749063 82 2 [0] [0] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1783818 1783881 64 2 [0] [1] 2 [hemP] [hemP]
* * ÷ NZ_CP009273 1807424 1807434 11 2 [0] [0] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1807508 1807566 59 3 [1] [1] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1839104 1839148 45 3 [1] [0] 5 [ynjI] [ynjI]
* * ÷ NZ_CP009273 1888062 1888129 68 2 [1] [1] 2 yoaB/yoaC RidA family protein/DUF1889 family protein
* * ÷ NZ_CP009273 1896179 1896205 27 2 [1] [1] 2 yoaE/manX CNNM family cation transport protein YoaE/PTS mannose transporter subunit IIAB
* * ÷ NZ_CP009273 1940370 1940482 113 3 [0] [0] 2 yobI yobI
* * ÷ NZ_CP009273 1960207 1960245 39 2 [1] [0] 3 flhB flagellar biosynthesis protein FlhB
* * ÷ NZ_CP009273 1973036 1973128 93 2 [1] [1] 2 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 2004728 2004760 33 4 [0] [0] 2 BW25113_RS10120 DUF5503 domain‑containing protein
* * ÷ NZ_CP009273 2004810 2004874 65 2 [0] [1] 2 BW25113_RS10120 DUF5503 domain‑containing protein
* * ÷ NZ_CP009273 2027317 2027439 123 3 [0] [1] 3 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2050181 2050275 95 2 [0] [1] 2 amn/yeeN AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 2051048 2051126 79 4 [1] [0] 2 [yeeN] [yeeN]
* * ÷ NZ_CP009273 2062007 2062107 101 2 [1] [1] 2 BW25113_RS10415/BW25113_RS24005 IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
* * ÷ NZ_CP009273 2093216 2093256 41 3 [1] [1] 4 ugd/gndA UDP‑glucose 6‑dehydrogenase/NADP‑dependent phosphogluconate dehydrogenase
* * ÷ NZ_CP009273 2096869 2096933 65 2 [1] [1] 2 [wbbL]–[wbbK] [wbbL],[wbbK]
* * ÷ NZ_CP009273 2097481 2097592 112 2 [1] [1] 3 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2099582 2099701 120 2 [1] [1] 5 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2100166 2100168 3 4 [0] [0] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2101599 2101651 53 3 [1] [1] 2 glf UDP‑galactopyranose mutase
* * ÷ NZ_CP009273 2144493 2144532 40 2 [0] [1] 2 yegI/yegJ protein kinase YegI/DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2144680 2144684 5 3 [0] [0] 2 yegJ DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2243117 2243166 50 2 [1] [0] 7 yeiE/yeiH DNA‑binding transcriptional regulator YeiE/YeiH family protein
* * ÷ NZ_CP009273 2300310 2300368 59 2 [0] [1] 3 mqo/yojI malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
* * ÷ NZ_CP009273 2337814 2337854 41 2 [1] [1] 2 yfaL/nrdA AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2359242 2359311 70 2 [1] [1] 3 ais/arnB lipopolysaccharide core heptose(II)‑phosphate phosphatase Ais/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase
* * ÷ NZ_CP009273 2449328 2449455 128 3 [1] [1] 2 yfcV/sixA fimbrial protein/phosphohistidine phosphatase SixA
* * ÷ NZ_CP009273 2457525 2457669 145 2 [0] [1] 3 [BW25113_RS12235] [BW25113_RS12235]
* * ÷ NZ_CP009273 2462831 2462834 4 2 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2462883 2462926 44 2 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463180 2463190 11 2 [0] [0] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463616 2463763 148 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2569341 2569354 14 2 [0] [1] 2 eutS/maeB ethanolamine utilization microcompartment protein EutS/NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase
* * ÷ NZ_CP009273 2689220 2689236 17 3 [1] [1] 2 mltF membrane‑bound lytic murein transglycosylase MltF
* * ÷ NZ_CP009273 2753644 2753740 97 2 [1] [0] 2 yfjI YfjI family protein
* * ÷ NZ_CP009273 2767749 2767759 11 2 [0] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2768349 2768353 5 2 [0] [0] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2778555 2778573 19 2 [0] [1] 4 BW25113_RS25705/BW25113_RS13825 DUF5507 domain‑containing protein/tRNA‑Ile
* * ÷ NZ_CP009273 2779832 2779867 36 2 [1] [0] 2 BW25113_RS26005 alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2877640 2877695 56 3 [1] [0] 3 casA/cas3 type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
* * ÷ NZ_CP009273 2877738 2877791 54 3 [1] [1] 2 casA/cas3 type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
* * ÷ NZ_CP009273 2897143 2897225 83 2 [1] [1] 3 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2975685 2975705 21 2 [1] [0] 2 araE/kduD arabinose‑proton symporter AraE/2‑dehydro‑3‑deoxy‑D‑gluconate 5‑dehydrogenase KduD
* * ÷ NZ_CP009273 2984546 2984609 64 2 [0] [1] 3 BW25113_RS14825/ygeG hypothetical protein/tetratricopeptide repeat protein
* * ÷ NZ_CP009273 2988511 2988618 108 2 [0] [0] 3 BW25113_RS14850/BW25113_RS26010 response regulator transcription factor/hypothetical protein
* * ÷ NZ_CP009273 3072870 3072902 33 2 [1] [0] 2 cmtB/tkt PTS mannitol transporter subunit IIA/transketolase
* * ÷ NZ_CP009273 3127428 3127475 48 3 [0] [0] 2 yghS/yghT dTMP kinase/dTMP kinase
* * ÷ NZ_CP009273 3129928 3129962 35 2 [0] [1] 2 pitB/gss inorganic phosphate transporter PitB/bifunctional glutathionylspermidine amidase/synthase
* * ÷ NZ_CP009273 3165523 3165533 11 2 [0] [1] 4 ygiZ DUF2645 family protein
* * ÷ NZ_CP009273 3260759 3260759 1 2 [0] [0] 2 tdcR transcriptional activator TdcR
* * ÷ NZ_CP009273 3262291 3262301 11 2 [0] [0] 3 yhaC YhaC family protein
* * ÷ NZ_CP009273 3280613 3280680 68 3 [1] [0] 2 agaI/yraH galactosamine‑6‑phosphate isomerase/fimbrial protein
* * ÷ NZ_CP009273 3354473 3354481 9 2 [0] [1] 2 gltD/gltF glutamate synthase subunit GltD/DUF1120 domain‑containing protein
* * ÷ NZ_CP009273 3378722 3378776 55 3 [1] [1] 3 argR/yhcN transcriptional regulator ArgR/peroxide/acid stress response protein YhcN
* * ÷ NZ_CP009273 3448830 3448903 74 3 [1] [0] 2 gspA/gspC type II secretion system protein GspA/type II secretion system protein GspC
* * ÷ NZ_CP009273 3575106 3575136 31 2 [0] [0] 3 yhhY/hcp N‑acetyltransferase/Hcp1 family type VI secretion system effector
* * ÷ NZ_CP009273 3575462 3575536 75 2 [1] [0] 2 hcp Hcp1 family type VI secretion system effector
* * ÷ NZ_CP009273 3576022 3576022 1 2 [0] [0] 3 hcp Hcp1 family type VI secretion system effector
* * ÷ NZ_CP009273 3576413 3576548 136 2 [1] [1] 2 BW25113_RS17825 YrhA family protein
* * ÷ NZ_CP009273 3790378 3790413 36 2 [1] [1] 2 waaL O‑antigen ligase
* * ÷ NZ_CP009273 3792569 3792642 74 2 [0] [0] 2 waaU glycosyltransferase family 9 protein
* * ÷ NZ_CP009273 3792729 3792779 51 4 [0] [1] 3 waaZ 3‑deoxy‑D‑manno‑oct‑2‑ulosonate III transferase WaaZ
* * ÷ NZ_CP009273 3797730 3797732 3 3 [0] [0] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3797774 3797831 58 2 [0] [1] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3798196 3798240 45 3 [1] [1] 3 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3943538 3943585 48 4 [0] [1] 3 yifB/ilvL YifB family Mg chelatase‑like AAA ATPase/ilv operon leader peptide
* * ÷ NZ_CP009273 3979448 3979479 32 2 [1] [0] 2 aslA/hemY arylsulfatase AslA/protoheme IX biogenesis protein HemY
* * ÷ NZ_CP009273 4037441 4037473 33 3 [1] [0] 4 dsbA/yihF thiol:disulfide interchange protein DsbA/YdgA family protein
* * ÷ NZ_CP009273 4250280 4250307 28 3 [1] [0] 2 BW25113_RS21020 DUF2713 domain‑containing protein
* * ÷ NZ_CP009273 4296625 4296633 9 2 [1] [0] 4 yjcS/alsK alkyl sulfatase YjcS/allose kinase
* * ÷ NZ_CP009273 4302908 4302954 47 2 [1] [1] 2 alsR/rpiB als operon DNA‑binding transcriptional repressor AlsR/bifunctional allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase RpiB
* * ÷ NZ_CP009273 4316819 4316830 12 3 [0] [0] 2 yjdM/crfC zinc ribbon domain‑containing protein YjdM/clamp‑binding protein CrfC
* * ÷ NZ_CP009273 4327851 4327896 46 2 [1] [1] 2 adiY/adiA DNA‑binding transcriptional activator AdiY/arginine decarboxylase
* * ÷ NZ_CP009273 4330444 4330487 44 3 [1] [1] 2 adiA/melR arginine decarboxylase/transcriptional regulator MelR
* * ÷ NZ_CP009273 4364119 4364158 40 3 [1] [0] 2 yjeJ/epmB YjeJ family protein/EF‑P beta‑lysylation protein EpmB
* * ÷ NZ_CP009273 4427367 4427391 25 6 [1] [0] 2 cysQ/BW25113_RS21900 3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein
* * ÷ NZ_CP009273 4466797 4466899 103 2 [1] [0] 2 BW25113_RS22080 hypothetical protein
* * ÷ NZ_CP009273 4487817 4487841 25 2 [1] [1] 2 BW25113_RS22170/BW25113_RS22180 tyrosine‑type recombinase/integrase/IS3‑like element IS2 family transposase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)24 (1.200) 15/166 0.3 64.9% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 13 (0.650)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 = 120326110 (0.500)5 (0.310) 5/134 1.0 35.6% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 10 (0.620)coding (57/540 nt) BW25113_RS06005 phage tail protein