breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 70,659 G→A W91* (TGG→TGA)  araC → DNA‑binding transcriptional dual regulator AraC
RA 100,946 T→C M61T (ATG→ACG)  murC → UDP‑N‑acetylmuramate‑‑L‑alanine ligase
RA 244,775 G→A G150D (GGC→GAC)  yafJ → putative glutamine amidotransferase YafJ
RA 245,662 G→A I48I (ATC→ATT)  dpaA ← peptidoglycan meso‑diaminopimelic acid protein amidase A
RA 246,747 G→T S12S (TCG→TCT)  yafL → NlpC/P60 family protein YafL
RA 248,203 G→A intergenic (+69/‑2695) rayT → / → dinB REP‑associated tyrosine transposase/DNA polymerase IV
RA 250,009 G→A intergenic (+1875/‑889) rayT → / → dinB REP‑associated tyrosine transposase/DNA polymerase IV
RA 251,629 C→T G244G (GGC→GGT)  dinB → DNA polymerase IV
RA 365,306 G→A R334C (CGC→TGC)  lacZ ← beta‑galactosidase
RA 480,295 2 bp→AA coding (13‑14/219 nt) hha ← hemolysin expression‑modulating protein Hha
RA 690,948 G→A V279V (GTC→GTT)  ybeX ← CorC‑HlyC family protein YbeX
RA 700,038 G→A H97Y (CAT→TAT)  umpH ← UMP phosphatase
RA 809,217 2 bp→AG coding (40‑41/1290 nt) bioA ← adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase
RA 968,837 G→A D158N (GAT→AAT)  lpxK → tetraacyldisaccharide 4'‑kinase
RA 1,061,935 G→A S46N (AGC→AAC)  torD → trimethylamine‑N‑oxide reductase‑specific chaperone
RA 1,069,743 C→T A33T (GCA→ACA)  rutG ← pyrimidine:H(+) symporter
RA 1,093,346 (T)6→5 coding (471/1359 nt) dgcT → putative diguanylate cyclase DgcT
RA 1,098,620 T→A V245V (GTT→GTA)  ghrA → glyoxylate/hydroxypyruvate reductase A
RA 1,111,727 2 bp→TT coding (865‑866/2544 nt) opgH → osmoregulated periplasmic glucans biosynthesis protein H
RA 1,169,836 A→G L180P (CTG→CCG)  ldtC ← L,D‑transpeptidase LdtC
RA 1,189,980 A→G T156T (ACT→ACC)  phoP ← DNA‑binding transcriptional dual regulator PhoP
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase
RA 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase
RA 1,196,245 T→C L375M (TTA→CTG)  icd → isocitrate dehydrogenase
RA 1,196,247 A→G L375M (TTA→CTG)  icd → isocitrate dehydrogenase
JC JC 1,271,657 IS5 (+) +4 bp coding (190‑193/1101 nt) chaA ← Na(+)/K(+):H(+) antiporter ChaA
RA 1,301,992 A→T N271Y (AAT→TAT)  oppA → oligopeptide ABC transporter periplasmic binding protein
RA 1,306,736 T→G S325A (TCC→GCC)  oppF → murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF
RA 1,310,770 A→G H32H (CAT→CAC)  yciI ← protein YciI
RA 1,337,394 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1
RA 1,357,202 C→T intergenic (‑92/+221) sapA ← / ← ymjA putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA
RA 1,358,859 T→C Y110C (TAT→TGT)  puuP ← putrescine:H(+) symporter PuuP
RA 1,539,947 C→G A882P (GCG→CCG)  narZ ← nitrate reductase Z subunit alpha
RA 1,643,679 A→T L209Q (CTG→CAG)  ydfU ← protein YdfU
RA 1,652,331 T→C intergenic (+2346/+397) ydfD → / ← ynfP lysis protein/protein YnfP
RA 1,728,754 C→T A136A (GCC→GCT)  rnt → ribonuclease T
RA 1,829,887 G→A A293A (GCC→GCT)  astA ← arginine N‑succinyltransferase
RA 1,894,839 T→C L12P (CTC→CCC)  pabB → aminodeoxychorismate synthase subunit 1
JC JC 1,907,641 IS5 (+) +4 bp intergenic (‑50/+617) yobF ← / ← yebO DUF2527 domain‑containing protein YobF/uncharacterized protein YebO
RA 1,978,437 G→A intergenic (‑240/+81) flhD ← / ← insB5 DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
MC JC 1,978,503 Δ776 bp insB5–insA5 insB5, insA5
RA 2,040,433 C→A A319D (GCC→GAC)  msrP → protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP
RA 2,042,171 G→A intergenic (+146/‑197) zinT → / → yodB metal‑binding protein ZinT/putative cytochrome b561 YodB
RA 2,044,642 T→C intergenic (+18/‑296) asnT → / → yeeJ tRNA‑Asn/inverse autotransporter adhesin
RA 2,111,259 Δ1 bp coding (718/900 nt) rfbD ← dTDP‑4‑dehydrorhamnose reductase
RA 2,173,363 Δ2 bp intergenic (‑490/+918) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
RA 2,173,448 C→T intergenic (‑575/+834) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
JC JC 2,175,525 IS1 (+) +8 bp coding (790‑797/1263 nt) gatZ ← putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone
RA 2,339,173 G→A S83L (TCG→TTG)  gyrA ← DNA gyrase subunit A
JC JC 2,375,828 IS186 (–) +4 bp coding (132‑135/963 nt) menC ← o‑succinylbenzoate synthase
JC JC 2,468,298 IS3 (+) +3 bp coding (85‑87/921 nt) yfdH → bactoprenol glucosyl transferase
MC JC 2,558,699 Δ6,790 bp intZ–[eutA] intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA]
RA 2,587,112 C→T A461V (GCA→GTA)  narQ → sensor histidine kinase NarQ
RA 2,661,961 G→T S57R (AGC→AGA)  iscR ← DNA‑binding transcriptional dual regulator IscR
RA 2,680,490 G→A C752C (TGC→TGT)  yphG ← DUF5107 domain‑containing protein YphG
RA 2,686,156 G→A E108K (GAA→AAA)  hmp → nitric oxide dioxygenase
RA 2,724,285 G→A R53Q (CGG→CAG)  yfiM → DUF2279 domain‑containing protein YfiM
RA 2,729,586 G→A intergenic (‑142/+30) gltW ← / ← rrsG tRNA‑Glu/16S ribosomal RNA
RA 2,823,537 A→G L78P (CTG→CCG)  recA ← DNA recombination/repair protein RecA
RA 2,867,454 2 bp→AA coding (97‑98/993 nt) rpoS ← RNA polymerase sigma factor RpoS
RA 2,926,772 C→A G155G (GGC→GGA)  ppnN → nucleotide 5'‑monophosphate nucleosidase
RA 2,939,297 G→T G137V (GGG→GTG)  fucU → L‑fucose mutarotase
RA 2,942,663 G→A intergenic (‑96/‑33) gcvA ← / → gcvB DNA‑binding transcriptional dual regulator GcvA/small regulatory RNA GcvB
RA 3,152,494 G→T A87S (GCG→TCG)  metC → cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase
JC JC 3,189,672 IS5 (–) +4 bp pseudogene (2241‑2244/2434 nt) yqiG → putative outer membrane usher protein YqiG
RA 3,207,549 Δ1 bp coding (179/606 nt) ttdB → L(+)‑tartrate dehydratase subunit beta
RA 3,329,743 G→T D261Y (GAT→TAT)  dacB → peptidoglycan DD‑endopeptidase DacB
JC JC 3,350,556 IS1 (–) +8 bp intergenic (‑97/‑14) elbB ← / → arcZ low activity glyoxalase ElbB/small regulatory RNA ArcZ
RA 3,388,041 T→G T50P (ACG→CCG)  aaeB ← aromatic carboxylic acid efflux pump subunit AaeB
JC JC 3,429,986 IS3 (–) +5 bp :: +T coding (34‑38/258 nt) yrdB ← DUF1488 domain‑containing protein YrdB
RA 3,560,443 C→G intergenic (+577/+179) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 3,560,455 +G intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 3,683,483 G→T intergenic (‑36/+147) dctA ← / ← pdeK C4 dicarboxylate/orotate:H(+) symporter/c‑di‑GMP phosphodiesterase PdeK
RA 3,707,878 A→G intergenic (‑173/+738) dppA ← / ← proK dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro
RA 3,707,883 G→A intergenic (‑178/+733) dppA ← / ← proK dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro
RA 3,707,947 C→A intergenic (‑242/+669) dppA ← / ← proK dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro
RA 3,725,176 T→G E48A (GAG→GCG)  glyQ ← glycine‑‑tRNA ligase subunit alpha
JC 3,755,733 Δ3 bp coding (777‑779/1539 nt) aldB ← aldehyde dehydrogenase B
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
JC JC 3,888,869 IS1 (+) +9 bp coding (140‑148/1416 nt) tnaA → tryptophanase
JC JC 3,902,169 IS5 (+) +4 bp coding (49‑52/1617 nt) bglH ← carbohydrate‑specific outer membrane porin, cryptic
RA 4,154,691 G→A Q53* (CAG→TAG)  argE ← acetylornithine deacetylase
RA 4,182,576 T→G D444E (GAT→GAG)  rpoB → RNA polymerase subunit beta
RA 4,182,782 A→T Q513L (CAG→CTG)  rpoB → RNA polymerase subunit beta
RA 4,212,973 Δ1 bp intergenic (+27/‑67) rrlE → / → rrfE 23S ribosomal RNA/5S ribosomal RNA
RA 4,220,685 A→G F601F (TTT→TTC)  arpA ← regulator of acetyl CoA synthetase
RA 4,223,638 T→C intergenic (‑10/‑190) iclR ← / → metH DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase
RA 4,287,464 T→A intergenic (‑93/‑147) acs ← / → ytcB acetyl‑CoA synthetase (AMP‑forming)/protein YtcB
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,325,644 C→T S33N (AGC→AAC)  yjdN ← PF06983 family protein YjdN
RA 4,473,900 C→T G52R (GGA→AGA)  bdcA ← c‑di‑GMP‑binding biofilm dispersal mediator protein
RA 4,475,493 T→C F19F (TTT→TTC)  yjgL → protein YjgL
RA 4,510,238 T→G intergenic (+445/+452) insO → / ← fecE IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit
RA 4,532,409 T→G intergenic (‑758/+28) sgcX ← / ← yjhP putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP
JC JC 4,542,469 IS1 (+) +9 bp coding (433‑441/597 nt) fimE → regulator for fimA
RA 4,546,601 C→T I502I (ATC→ATT)  fimD → type I fimbriae usher protein
RA 4,636,925 G→C R77P (CGC→CCC)  creC → sensory histidine kinase CreC
RA 4,638,240 G→A L21L (TTG→TTA)  creD → putative inner membrane protein CreD

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 256108 276207 20100 19 [0] [3] 4 [gpt]–[mmuP] [gpt],frsA,crl,insB9,insA9,crl,phoE,proB,proA,thrW,ykfI,yafW,ykfH,ykfG,yafX,ykfF,ykfB,yafY,yafZ,ykfA,perR,insN,insI1,insN,eyeA,ykfC,insH1,[mmuP]
* * ÷ NC_000913 276327 277862 1536 4 [2] [3] 4 [mmuP]–[afuC] [mmuP],mmuM,[afuC]
* * ÷ NC_000913 278520 280401 1882 4 [3] [3] 4 [afuC]–[yagB] [afuC],insB2,insA2,[yagB]
* * ÷ NC_000913 280407 283542 3136 4 [3] [3] 4 [yagB]–[yagF] [yagB],yagA,yagE,[yagF]
* * ÷ NC_000913 283747 286678 2932 4 [3] [2] 4 [yagF]–[yagG] [yagF],[yagG]
* * ÷ NC_000913 286689 288754 2066 4 [3] [3] 4 [yagG]–[xynR] [yagG],yagH,[xynR]
* * ÷ NC_000913 288812 292082 3271 4 [3] [3] 4 [xynR]–[yagJ] [xynR],argF,argL,ykgS,insB3,insA3,[yagJ]
* * ÷ NC_000913 292480 297948 5469 4 [3] [3] 4 [yagK]–[paoD] [yagK],yagL,yagM,ykgV,yagN,intF,yagP,[paoD]
* * ÷ NC_000913 298184 300199 2016 4 [3] [2] 4 [paoD]–[paoC] [paoD],[paoC]
* * ÷ NC_000913 300414 304655 4242 4 [3] [3] 4 [paoC]–[ecpE] [paoC],paoB,paoA,yagU,ykgJ,[ecpE]
* * ÷ NC_000913 304762 306375 1614 4 [3] [2] 4 [ecpE]–[ecpD] [ecpE],[ecpD]
* * ÷ NC_000913 306603 306992 390 4 [3] [3] 4 [ecpD]–[ecpC] [ecpD],[ecpC]
* * ÷ NC_000913 307215 315228 8014 4 [3] [3] 36 [ecpC]–ykgR [ecpC],ecpB,ecpA,matA,ykgL,ykgO,ykgM,ykgR
* * ÷ NC_000913 316631 318801 2171 4 [3] [2] 4 rclC–[rclA] rclC,rclB,[rclA]
* * ÷ NC_000913 318948 319492 545 4 [3] [3] 4 rclA cupric reductase RclA
* * ÷ NC_000913 319528 320268 741 4 [3] [3] 5 [rclA]–[rclR] [rclA],[rclR]
* * ÷ NC_000913 320364 322014 1651 4 [3] [2] 4 [rclR]–[ykgE] [rclR],[ykgE]
* * ÷ NC_000913 322162 323474 1313 4 [2] [2] 4 [ykgE]–[ykgF] [ykgE],[ykgF]
* * ÷ NC_000913 323754 324911 1158 4 [3] [3] 4 [ykgF]–[ykgH] [ykgF],ykgG,[ykgH]
* * ÷ NC_000913 325046 325714 669 4 [3] [3] 4 [ykgH]–[betA] [ykgH],[betA]
* * ÷ NC_000913 325782 326191 410 4 [3] [3] 4 betA choline dehydrogenase
* * ÷ NC_000913 326681 329238 2558 5 [3] [3] 5 [betA]–[betI] [betA],betB,[betI]
* * ÷ NC_000913 329337 329997 661 4 [3] [3] 4 [betT] [betT]
* * ÷ NC_000913 330529 333251 2723 4 [3] [3] 4 [betT]–[pdeL] [betT],yahV,[pdeL]
* * ÷ NC_000913 333744 335507 1764 4 [3] [3] 4 [yahB]–[yahD] [yahB],yahC,[yahD]
* * ÷ NC_000913 335619 336263 645 4 [2] [2] 4 [yahD]–[yahE] [yahD],[yahE]
* * ÷ NC_000913 336651 338742 2092 4 [2] [3] 4 [yahE]–[yahG] [yahE],yahF,[yahG]
* * ÷ NC_000913 338814 339631 818 4 [3] [3] 4 yahG DUF1116 domain‑containing protein YahG
* * ÷ NC_000913 339898 341867 1970 5 [3] [3] 4 [yahH]–[yahJ] [yahH],yahI,[yahJ]
* * ÷ NC_000913 343314 344205 892 4 [3] [3] 4 [yahK]–[yahL] [yahK],[yahL]
* * ÷ NC_000913 344419 344956 538 4 [3] [1] 5 yahL uncharacterized protein YahL
* * ÷ NC_000913 345181 348131 2951 6 [2] [3] 4 yahM–[prpR] yahM,yahN,yahO,[prpR]
* * ÷ NC_000913 348521 349826 1306 4 [3] [3] 4 prpB prpB
* * ÷ NC_000913 351863 353099 1237 4 [3] [3] 4 [prpD]–[prpE] [prpD],[prpE]
* * ÷ NC_000913 353352 356768 3417 4 [3] [2] 4 [prpE]–[codA] [prpE],codB,[codA]
* * ÷ NC_000913 357317 358865 1549 4 [3] [2] 4 [codA]–[cynT] [codA],cynR,[cynT]
* * ÷ NC_000913 358915 362651 3737 4 [3] [3] 4 [cynT]–[lacY] [cynT],cynS,cynX,lacA,[lacY]
* * ÷ NC_000913 362820 363319 500 4 [3] [3] 5 [lacY]–[lacZ] [lacY],[lacZ]
* * ÷ NC_000913 363764 364878 1115 4 [3] [3] 4 lacZ beta‑galactosidase
* * ÷ NC_000913 365860 366180 321 4 [3] [3] 4 lacZ beta‑galactosidase
* * ÷ NC_000913 366508 368338 1831 4 [3] [3] 5 [lacI]–[mhpR] [lacI],[mhpR]
* * ÷ NC_000913 368438 369290 853 4 [3] [3] 4 [mhpA] [mhpA]
* * ÷ NC_000913 369344 369860 517 4 [3] [3] 4 mhpA 3‑(3‑hydroxyphenyl)propanoate hydroxylase
* * ÷ NC_000913 370018 370384 367 4 [3] [3] 4 [mhpA]–[mhpB] [mhpA],[mhpB]
* * ÷ NC_000913 683091 685401 2311 21 [1] [3] 4 [hscC]–[gltK] [hscC],rihA,gltL,[gltK]
* * ÷ NC_000913 685574 686213 640 5 [3] [2] 4 [gltK]–[gltJ] [gltK],[gltJ]
* * ÷ NC_000913 686415 688817–687846 1432–2403 4 [3] [3] 5 [gltJ]–[insH3] [gltJ],sroC,gltI,[insH3]
* * ÷ NC_000913 707978 708059 82 4 [3] [3] 4 glnS/chiZ glutamine‑‑tRNA ligase/small regulatory RNA ChiZ
* * ÷ NC_000913 1196323 1211412 15090 4 [3] [0] 4 [icd]–mcrA [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA
* * ÷ NC_000913 1813186 1813301 116 4 [3] [2] 4 ydjO/cedA protein YdjO/cell division modulator
* * ÷ NC_000913 2011986 2012155 170 4 [3] [3] 4 yedL/fliE putative acetyltransferase YedL/flagellar protein FliE
* * ÷ NC_000913 2878205 2878332 128 4 [3] [2] 4 iap/cas2 alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2
* * ÷ NC_000913 2903741 2903941 201 4 [3] [2] 4 ygcE/queE putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NC_000913 2995173 2995242 70 4 [2] [3] 4 ygeI/insD4 protein YgeI/IS2 insertion element protein InsB
* * ÷ NC_000913 3268755 3268942 188 4 [3] [2] 4 yhaC uncharacterized protein YhaC
* * ÷ NC_000913 3269074 3269271 198 4 [2] [2] 4 yhaC uncharacterized protein YhaC
* * ÷ NC_000913 3423873–3424231 3424428–3424238 8–556 4 [3] [3] 4 [rrlD] [rrlD]
* * ÷ NC_000913 3798896 3799280 385 4 [3] [3] 4 waaU putative ADP‑heptose:LPS heptosyltransferase 4
* * ÷ NC_000913 4035362–4035722 4036852–4035735 14–1491 4 [3] [3] 4 [rrsA] [rrsA]
* * ÷ NC_000913 4166879–4168219 4168497 279–1619 4 [3] [3] 4 [rrsB]–gltT [rrsB],gltT

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 15911NA (NA)6 (0.170)
+TTTTTTCAA		 6/468 2.1 NA noncoding (525/1345 nt) IS186 repeat region
?NC_000913 15922 = NA (NA)noncoding (536/1345 nt) IS186 repeat region
* ? NC_000913 = 2561070 (0.000)19 (0.540) 18/470 0.7 97.4% coding (131/459 nt) gpt xanthine‑guanine phsophoribosyltransferase
?NC_000913 371382 = 1 (0.030)coding (144/867 nt) mhpC 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase
* ? NC_000913 = 56677437 (1.020)39 (1.090) 22/482 0.5 51.4% pseudogene (91/93 nt) renD protein RenD
?NC_000913 568036 = 37 (1.030)pseudogene (2/213 nt) renD protein RenD
* ? NC_000913 = 6830901 (0.030)20 (0.550) 19/486 0.7 95.2% coding (304/1671 nt) hscC chaperone protein HscC
?NC_000913 687851 = NA (NA)noncoding (1195/1195 nt) IS5 repeat region
* ? NC_000913 = 28782180 (0.000)3 (0.090) 3/428 2.8 100% intergenic (+600/+351) iap/cas2 alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2
?NC_000913 2878281 = 0 (0.000)intergenic (+663/+288) iap/cas2 alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2