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 160,220 G→A R129C (CGC→TGC)  dksA ← RNA polymerase‑binding transcription factor DksA
RA 246,747 G→T S12S (TCG→TCT)  yafL → NlpC/P60 family protein YafL
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 284,535 T→G A445A (GCT→GCG)  yagF → D‑xylonate dehydratase
RA 313,543 G→A intergenic (‑301/‑1748) ykgR ← / → insE1 putative membrane protein YkgR/IS3 element protein InsE
RA 339,935 C→T A56V (GCC→GTC)  yahH → putative uncharacterized protein YahH
RA 339,941 C→T T58I (ACT→ATT)  yahH → putative uncharacterized protein YahH
RA 339,958 G→A D64N (GAC→AAC)  yahH → putative uncharacterized protein YahH
RA 393,962 C→T pseudogene (993/1449 nt) yaiT → putative autotransporter YaiT
RA 465,005 G→A V181V (GTC→GTT)  queC ← 7‑cyano‑7‑deazaguanine synthase
RA 472,849 A→G G84G (GGA→GGG)  glnK → nitrogen regulatory protein PII‑2
RA 495,622 C→T T168I (ACC→ATC)  htpG → chaperone protein HtpG
RA 534,742 G→A G276D (GGT→GAT)  gcl → glyoxylate carboligase
RA 578,331 G→T A75A (GCG→GCT) 
R2L (CGA→CTA) 		 rzpD →
rzoD →		 putative prophage endopeptidase RzpD
putative prophage lysis lipoprotein RzoD
RA 578,427 G→C T107T (ACG→ACC) 
R34P (CGG→CCG) 		 rzpD →
rzoD →		 putative prophage endopeptidase RzpD
putative prophage lysis lipoprotein RzoD
RA 578,571 C→T intergenic (+3/+29) rzpD → / ← borD putative prophage endopeptidase RzpD/prophage lipoprotein BorD
RA 578,574 A→C intergenic (+6/+26) rzpD → / ← borD putative prophage endopeptidase RzpD/prophage lipoprotein BorD
RA 578,605 T→G K97Q (AAA→CAA)  borD ← prophage lipoprotein BorD
RA 578,729 A→G A55A (GCT→GCC)  borD ← prophage lipoprotein BorD
RA 578,809 T→C T29A (ACA→GCA)  borD ← prophage lipoprotein BorD
RA 578,811 T→G Q28P (CAG→CCG)  borD ← prophage lipoprotein BorD
RA 578,831 T→C T21T (ACA→ACG)  borD ← prophage lipoprotein BorD
RA 579,004 C→T intergenic (‑111/+180) borD ← / ← ybcV prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
RA 579,099 (A)5→4 intergenic (‑206/+85) borD ← / ← ybcV prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
RA 579,127 T→C intergenic (‑234/+57) borD ← / ← ybcV prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
RA 579,134 T→C intergenic (‑241/+50) borD ← / ← ybcV prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
RA 579,146 A→G intergenic (‑253/+38) borD ← / ← ybcV prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
RA 582,597 C→T intergenic (+500/‑278) tfaD → / → tfaX putative tail fiber assembly protein TfaD/protein TfaX
RA 694,941 G→A L5L (CTC→CTT)  miaB ← isopentenyl‑adenosine A37 tRNA methylthiolase
RA 696,470 C→T noncoding (35/75 nt) glnX ← tRNA‑Gln
RA 708,774 G→A A147A (GCG→GCA)  chiP → chitooligosaccharide outer membrane channel
RA 721,604 G→A R44C (CGT→TGT)  kdpE ← DNA‑binding transcriptional activator KdpE
RA 780,624 C→T noncoding (71/76 nt) lysT → tRNA‑Lys
RA 789,580 C→A E134* (GAA→TAA)  galK ← galactokinase
RA 968,837 G→A D158N (GAT→AAT)  lpxK → tetraacyldisaccharide 4'‑kinase
RA 1,040,126 G→T L277L (CTG→CTT)  appB → cytochrome bd‑II subunit 2
RA 1,061,935 G→A S46N (AGC→AAC)  torD → trimethylamine‑N‑oxide reductase‑specific chaperone
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
RA 1,196,277 C→T N385N (AAC→AAT)  icd → isocitrate dehydrogenase
RA 1,196,280 G→C A386A (GCG→GCC)  icd → isocitrate dehydrogenase
RA 1,196,283 A→G K387K (AAA→AAG)  icd → isocitrate dehydrogenase
RA 1,196,292 C→T T390T (ACC→ACT)  icd → isocitrate dehydrogenase
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 1,308,684 T→C intergenic (‑39/‑104) clsA ← / → yciY cardiolipin synthase A/uncharacterized protein YciY
RA 1,331,059 2 bp→AT coding (12‑13/2598 nt) topA → DNA topoisomerase 1
RA 1,337,394 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1
RA 1,358,859 T→C Y110C (TAT→TGT)  puuP ← putrescine:H(+) symporter PuuP
RA 1,429,069 T→A G7G (GGT→GGA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,072 A→C V8V (GTA→GTC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,111 A→C T21T (ACA→ACC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,114 C→T I22I (ATC→ATT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,126 A→C A26A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,128 A→G K27R (AAA→AGA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,160 C→G L38V (CTG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,164 C→G A39G (GCC→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,171 A→G E41E (GAA→GAG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,204 C→T D52D (GAC→GAT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,207 T→G V53V (GTT→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,225 C→T S59S (AGC→AGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,228 T→C V60V (GTT→GTC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,231 T→C I61I (ATT→ATC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,235 2 bp→CA coding (187‑188/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,240 G→T V64V (GTG→GTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,243 A→C E65D (GAA→GAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,246 A→T G66G (GGA→GGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,249 C→T F67F (TTC→TTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,252 G→A P68P (CCG→CCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,255 G→A P69P (CCG→CCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,258 A→G S70S (TCA→TCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,261 T→C H71H (CAT→CAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,273 T→C I75I (ATT→ATC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,291 T→A S81S (TCT→TCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,297 C→G P83P (CCC→CCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,300 T→G G84G (GGT→GGG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,319 G→T G91C (GGT→TGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,345 T→G R99R (CGT→CGG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,353 2 bp→TG coding (305‑306/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,360 C→T R104R (CGC→CGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,364 T→C F106L (TTT→CTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,404 C→T A119V (GCG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,416 2 bp→GT coding (368‑369/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,425 C→A A126D (GCC→GAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,435 G→A K129K (AAG→AAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,442 A→G S132G (AGT→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,444 T→C S132G (AGT→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,453 2 bp→TG coding (405‑406/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,462 3 bp→TGC coding (414‑416/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,466 G→C E140Q (GAG→CAG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,470 2 bp→TC coding (422‑423/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,474 2 bp→GG coding (426‑427/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,479 A→T H144L (CAT→CTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,482 C→T A145V (GCG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,484 G→A A146T (GCT→ACT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,492 2 bp→AA coding (444‑445/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,495 G→T A149A (GCG→GCT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,510 A→C A154A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,522 A→C S158S (TCA→TCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,534 C→T A162A (GCC→GCT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,537 G→A A163A (GCG→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,543 G→A S165S (TCG→TCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,550 2 bp→GA coding (502‑503/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,558 T→C S170S (TCT→TCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,562 A→G S172G (AGC→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,569 G→A G174E (GGA→GAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,571 A→G T175A (ACG→GCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,580 A→G T178A (ACA→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,597 3 bp→GGA coding (549‑551/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,609 T→C A187A (GCT→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,612 C→A A188A (GCC→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,615 T→C A189A (GCT→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,632 G→A S195N (AGC→AAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,682 T→G S212A (TCA→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,692 T→A L215Q (CTA→CAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,702 A→C A218A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,708 A→G T220T (ACA→ACG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,714 A→C A222A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,724 A→G T226A (ACC→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,732 G→A K228K (AAG→AAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,735 A→G A229A (GCA→GCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,741 A→G E231E (GAA→GAG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,744 T→C A232A (GCT→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,747 G→C A233A (GCG→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,750 C→T T234T (ACC→ACT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,753 G→A S235S (TCG→TCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,756 C→A A236A (GCC→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,759 G→A R237R (CGG→CGA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,767 C→T A240V (GCG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,780 A→G E244E (GAA→GAG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,783 G→A A245A (GCG→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,816 C→T S256S (AGC→AGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,820 A→G S258G (AGT→GGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,823 A→C S259R (AGT→CGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,591,711 C→A E156* (GAG→TAG)  hipA ← serine/threonine‑protein kinase toxin HipA
RA 1,629,247 C→T I11I (ATC→ATT)  ydfZ → putative selenoprotein YdfZ
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 1,721,136 C→T L38F (CTT→TTT)  ydhI → DUF1656 domain‑containing protein YdhI
MC JC 1,757,511 Δ42 bp coding (91‑132/237 nt) lpp → murein lipoprotein
RA 1,776,715 A→T S377C (AGT→TGT)  ydiF → putative acetate‑CoA transferase YdiF
RA 1,894,839 T→C L12P (CTC→CCC)  pabB → aminodeoxychorismate synthase subunit 1
JC JC 1,907,165 IS150 (–) +3 bp intergenic (‑105/+59) rlmA ← / ← cspC 23S rRNA m(1)G745 methyltransferase/transcription antiterminator and regulator of mRNA stability CspC
RA 2,040,433 C→A A319D (GCC→GAC)  msrP → protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP
RA 2,120,969 G→A L196L (CTG→TTG)  wcaJ ← UDP‑glucose:undecaprenyl‑phosphate glucose‑1‑phosphate transferase
RA 2,142,598 G→A L117L (CTC→CTT)  udk ← uridine/cytidine kinase
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
RA 2,233,609 C→T Q4* (CAG→TAG)  yeiS → DUF2542 domain‑containing protein YeiS
JC JC 2,239,316 IS5 (–) +4 bp intergenic (‑27/+31) mglA ← / ← mglB D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit/D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein
RA 2,242,247 C→T G241R (GGG→AGG)  yeiB ← DUF418 domain‑containing protein YeiB
RA 2,247,134 A→C Y467D (TAC→GAC)  lysP ← lysine:H(+) symporter
RA 2,391,119 G→A F129F (TTC→TTT)  nuoN ← NADH:quinone oxidoreductase subunit N
RA 2,392,587 A→C F152C (TTC→TGC)  nuoM ← NADH:quinone oxidoreductase subunit M
RA 2,404,402 G→A S71L (TCG→TTG)  nuoB ← NADH:quinone oxidoreductase subunit B
RA 2,452,389 2 bp→AA intergenic (‑53/+2693) yfcS ← / ← yfcV putative fimbrial chaperone YfcS/putative fimbrial protein YfcV
RA 2,481,608 A→G L190S (TTA→TCA)  emrY ← tripartite efflux pump membrane subunit EmrY
RA 2,498,392 A→C intergenic (‑97/‑279) alaC ← / → pyrS glutamate‑‑pyruvate aminotransferase AlaC/sensor histidine kinase PyrS
RA 2,514,457 C→T L43L (CTG→TTG)  insL3 → putative IS186/IS421 transposase
RA 2,546,804 T→A D44E (GAT→GAA)  murP → N‑acetylmuramic acid‑specific PTS enzyme IICB component/anhydro‑N‑acetylmuramic acid transporter
MC JC 2,558,699 Δ6,790 bp intZ–[eutA] intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA]
RA 2,577,937 T→C E147E (GAA→GAG)  maeB ← malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+))
RA 2,587,112 C→T A461V (GCA→GTA)  narQ → sensor histidine kinase NarQ
RA 2,745,600 A→G Y107H (TAC→CAC)  rimM ← ribosome maturation factor RimM
RA 2,774,947 G→A G544S (GGT→AGT)  yfjW → uncharacterized protein YfjW
RA 2,787,591 A→G intergenic (‑1754/‑1394) ileY ← / → glaH tRNA‑Ile/glutarate dioxygenase GlaH
RA 2,867,455 G→A Q33* (CAG→TAG)  rpoS ← RNA polymerase sigma factor RpoS
JC JC 2,876,678 IS5 (–) +4 bp coding (98‑101/1038 nt) iap → alkaline phosphatase isozyme conversion protein
RA 2,880,635 T→C L138L (TTA→TTG)  casD ← type I‑E CRISPR system Cascade subunit CasD
RA 2,926,772 C→A G155G (GGC→GGA)  ppnN → nucleotide 5'‑monophosphate nucleosidase
RA 3,025,601 (T)5→4 coding (1251/1401 nt) xanQ → xanthine:H(+) symporter XanQ
RA 3,070,858 T→G K129N (AAA→AAC)  fbaA ← fructose‑bisphosphate aldolase class II
MC JC 3,131,341 Δ128 bp IS5‑mediated yghQ ← putative transport protein YghQ
RA 3,207,549 Δ1 bp coding (179/606 nt) ttdB → L(+)‑tartrate dehydratase subunit beta
RA 3,213,233 G→C D63H (GAT→CAT)  rpoD → RNA polymerase sigma factor RpoD
RA 3,252,295 G→T intergenic (+285/‑9) yqjG → / → yhaH glutathionyl‑hydroquinone reductase YqjG/putative inner membrane protein
JC JC 3,262,484 IS5 (+) +4 bp coding (1174‑1177/1209 nt) tdcD ← propionate kinase
RA 3,275,902 A→T E207D (GAA→GAT)  garD → GarD
RA 3,296,481 G→A V25M (GTG→ATG)  dolP → division and outer membrane stress‑associated lipid‑binding lipoprotein
RA 3,329,743 G→T D261Y (GAT→TAT)  dacB → peptidoglycan DD‑endopeptidase DacB
RA 3,388,041 T→G T50P (ACG→CCG)  aaeB ← aromatic carboxylic acid efflux pump subunit AaeB
RA 3,411,689 G→T E13* (GAA→TAA)  yhdJ → DNA adenine methyltransferase
RA 3,433,900 C→T L71L (CTA→TTA)  def → peptide deformylase
RA 3,474,425 T→C K43R (AAA→AGA)  rpsL ← 30S ribosomal subunit protein S12
RA 3,486,175 G→A C19Y (TGC→TAC)  crp → DNA‑binding transcriptional dual regulator CRP
RA 3,486,502 C→T T128I (ACT→ATT)  crp → DNA‑binding transcriptional dual regulator CRP
RA 3,497,106 G→A G35D (GGC→GAC)  nirC → nitrite transporter NirC
RA 3,507,249 C→T D30N (GAC→AAC)  yhfT ← uncharacterized protein YhfT
RA 3,511,466 C→T V293V (GTG→GTA)  yhfZ ← putative DNA‑binding transcriptional regulator YhfZ
MC JC 3,535,343 Δ5 bp coding (522‑526/1353 nt) envZ ← sensor histidine kinase EnvZ
RA 3,555,047 2 bp→TG coding (1963‑1964/2706 nt) malT → DNA‑binding transcriptional activator MalT
RA 3,560,362 G→A intergenic (+496/+260) 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 3,623,644 A→C K82N (AAA→AAC)  yhhH → PF15631 family protein YhhH
RA 3,646,970 G→T Q224H (CAG→CAT)  gor → glutathione reductase (NADPH)
RA 3,647,428 C→T A377V (GCG→GTG)  gor → glutathione reductase (NADPH)
RA 3,707,947 C→A intergenic (‑242/+669) dppA ← / ← proK dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro
RA 3,719,429 G→A intergenic (‑385/‑49) yiaF ← / → yiaG DUF3053 domain‑containing protein YiaF/putative DNA‑binding transcriptional regulator YiaG
RA 3,721,455 C→T L86L (CTC→CTT)  insK → IS150 family conserved protein InsB
RA 3,725,176 T→G E48A (GAG→GCG)  glyQ ← glycine‑‑tRNA ligase subunit alpha
RA 3,729,440 2 bp→TT noncoding (105‑106/160 nt) xylZ ← small RNA XylZ
RA 3,730,560 C→T W69* (TGG→TAG)  xylA ← xylose isomerase
RA 3,769,744 T→C intergenic (+64/+499) yibV → / ← yibH PF15596 family protein YibV/inner membrane protein YibH
RA 3,770,539 C→T V281M (GTG→ATG)  yibH ← inner membrane protein YibH
RA 3,773,173 Δ1 bp coding (893/1914 nt) mtlA → mannitol‑specific PTS enzyme IICBA component
RA 3,773,176 C→T S299F (TCT→TTT)  mtlA → mannitol‑specific PTS enzyme IICBA component
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,817,167 C→T T164T (ACC→ACT)  yicC → putative RNase adaptor protein YicC
RA 3,866,301 A→G intergenic (‑28/+168) yidE ← / ← ibpB putative transport protein YidE/small heat shock protein IbpB
RA 3,866,311 G→A intergenic (‑38/+158) yidE ← / ← ibpB putative transport protein YidE/small heat shock protein IbpB
MC JC 3,890,274 Δ36 bp coding (39‑74/1248 nt) tnaB → tryptophan:H(+) symporter TnaB
RA 3,897,907 G→A M134I (ATG→ATA)  cbrB → putative inner membrane protein
RA 3,993,531 T→C R793R (CGT→CGC)  cyaA → adenylate cyclase
RA 4,143,988 G→A intergenic (+44/‑7) frwB → / → pflD putative PTS enzyme IIB component FrwB/putative formate acetyltransferase 2
RA 4,148,224 G→A P32S (CCC→TCC)  yijO ← putative DNA‑binding transcriptional regulator YijO
RA 4,165,712 C→A A95A (GCC→GCA)  murI → glutamate racemase
RA 4,180,208 C→G C71W (TGC→TGG)  rplJ → 50S ribosomal subunit protein L10
RA 4,193,996 T→G D70A (GAT→GCT)  thiE ← thiamine phosphate synthase
RA 4,201,066 G→A Q167Q (CAG→CAA)  yjaH → DUF1481 domain‑containing protein YjaH
RA 4,202,911 G→A S329N (AGT→AAT)  zraS → sensor histidine kinase ZraS
RA 4,204,541 G→A E408K (GAG→AAG)  zraR → DNA‑binding transcriptional activator ZraR
RA 4,208,132 G→A intergenic (‑600/‑15) purH ← / → rrsE bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA
RA 4,217,676 G→A A190T (GCG→ACG)  aceA → isocitrate lyase
RA 4,223,638 T→C intergenic (‑10/‑190) iclR ← / → metH DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase
RA 4,227,849 G→A S40N (AGC→AAC)  yjbB → putative inorganic phosphate export protein YjbB
RA 4,236,257 G→A intergenic (+109/‑5) yjbE → / → yjbF uncharacterized protein YjbE/lipoprotein YjbF
RA 4,241,458 G→A T266I (ACC→ATC)  xylE ← D‑xylose:H(+) symporter
RA 4,243,075 C→T G148S (GGT→AGT)  malG ← maltose ABC transporter membrane subunit MalG
RA 4,274,290 C→T H56Y (CAC→TAC)  ssb → ssDNA‑binding protein
RA 4,288,777 C→T D338D (GAC→GAT)  nrfA → cytochrome c552 nitrite reductase
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,307,052 C→T D250N (GAT→AAT)  alsK ← D‑allose kinase
RA 4,307,221 T→C L193L (CTA→CTG)  alsK ← D‑allose kinase
RA 4,325,644 C→T S33N (AGC→AAC)  yjdN ← PF06983 family protein YjdN
RA 4,331,890 C→T L463L (CTC→CTT)  proP → osmolyte:H(+) symporter ProP
RA 4,338,117 (A)8→9 intergenic (‑188/+137) adiY ← / ← adiA DNA‑binding transcriptional activator AdiY/arginine decarboxylase, degradative
JC JC 4,343,759 IS2 (–) +5 bp coding (391‑395/1422 nt) melB → melibiose:H(+)/Na(+)/Li(+) symporter
RA 4,437,890 C→T Q62* (CAG→TAG)  ytfI → protein YtfI
RA 4,447,046 A→T T979S (ACC→TCC)  tamB → translocation and assembly module subunit TamB
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 4,476,605 G→A S390N (AGC→AAC)  yjgL → protein YjgL
RA 4,489,016 C→T E350K (GAA→AAA)  yjgR ← DUF853 domain‑containing protein YjgR
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
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 506776 517161 10386 60 [19] [1] 92 [ybaK]–[fetB] [ybaK],chiX,ybaP,ybaQ,copA,copA,copA,glsA,ybaT,cueR,ybbJ,qmcA,fetA,[fetB]
* * ÷ NC_000913 574804–575790 578257–578111 2322–3454 31 [29] [29] 31 [insH2]–[rzpD] [insH2],nmpC,essD,rrrD,[rzpD]
* * ÷ NC_000913 1196300 1211463 15164 31 [28] [29] 30 [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 1399594 1429027 29434 678 [2] [29] 30 ogt–lomR ogt,abgT,abgB,abgA,abgR,mcaS,smrA,dgcM,ynaN,zntB,fnrS,ynaL,dbpA,ttcA,intR,xisR,rcbA,ralA,ralR,recT,recE,racC,ydaE,kilR,kilS,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,ydaW,rzoR,trkG,ynaK,ydaY,ynaA,lomR,insH5,lomR
* * ÷ NC_000913 1429833 1459405 29573 30 [29] [0] 84 [stfR]–[paaH] [stfR],tfaR,pinR,ynaE,ynaM,uspF,ompN,micC,ydbK,ydbJ,hslJ,ldhA,ydbH,ynbE,ydbL,feaR,feaB,tynA,paaZ,paaA,paaB,paaC,paaD,paaE,paaF,paaG,[paaH]
* * ÷ NC_000913 1978495 1979270 776 91 [0] [0] 98 insB5–insA5 insB5,insA5
* * ÷ NC_000913 3423884–3424233 3424482–3424238 6–599 30 [29] [27] 30 rrlD 23S ribosomal RNA
* * ÷ NC_000913 4325909 4326299 391 30 [29] [28] 30 yjdN/yjdM PF06983 family protein YjdN/zinc ribbon domain‑containing protein YjdM

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 275149NA (NA)41 (0.450) 33/590 1.4 68.3% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 506775 19 (0.210)coding (308/480 nt) ybaK Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK
* ? NC_000913 = 275149NA (NA)97 (1.060) 62/590 0.1 48.7% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 579184 = 102 (1.110)coding (411/411 nt) ybcV DUF1398 domain‑containing protein YbcV
* ? NC_000913 381260 =NA (NA)30 (0.330) 23/588 2.5 30.9% noncoding (1/1331 nt) IS2 repeat region
?NC_000913 = 1186823 67 (0.730)coding (980/1227 nt) pepT peptidase T
* ? NC_000913 517162 =0 (0.000)91 (1.000) 53/588 0.3 100% coding (580/780 nt) fetB putative iron ABC exporter membrane subunit FetB
?NC_000913 574591 = NA (NA)noncoding (1195/1195 nt) IS5 repeat region
* ? NC_000913 = 566774128 (1.400)51 (0.560) 22/586 2.7 30.3% pseudogene (91/93 nt) renD protein RenD
?NC_000913 568036 = 108 (1.190)pseudogene (2/213 nt) renD protein RenD
* ? NC_000913 = 85520838 (0.420)44 (0.500) 34/572 1.2 54.4% coding (537/921 nt) ldtB L,D‑transpeptidase LdtB
?NC_000913 855563 = 37 (0.420)coding (182/921 nt) ldtB L,D‑transpeptidase LdtB
* ? NC_000913 = 109704023 (0.250)29 (0.440) 22/430 1.5 57.0% intergenic (+211/+525) ycdU/serX uncharacterized protein YcdU/tRNA‑Ser
?NC_000913 1097584 = 27 (0.410)noncoding (69/88 nt) serX tRNA‑Ser
* ? NC_000913 = 12994985 (0.050)111 (1.230) 60/582 0.2 97.8% intergenic (+253/‑69) ychE/insH21 MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 1396019 =NA (NA)669 (7.330) 185/588 0.0 100% intergenic (‑97/‑93) ynaI/insH4 small conductance mechanosensitive channel YnaI/IS5 family transposase and trans‑activator
?NC_000913 = 1399593 0 (0.000)intergenic (‑67/+128) fnr/ogt DNA‑binding transcriptional dual regulator FNR/methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase
* ? NC_000913 = 1397238NA (NA)90 (0.980) 56/590 0.3 100% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 1978494 0 (0.000)intergenic (‑297/+24) flhD/insB5 DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
* ? NC_000913 1459406 =0 (0.000)84 (0.920) 56/590 0.3 100% coding (353/1428 nt) paaH 3‑hydroxyadipyl‑CoA dehydrogenase
?NC_000913 2101749 = NA (NA)noncoding (1195/1195 nt) IS5 repeat region
* ? NC_000913 1469296 =NA (NA)29 (0.320) 27/586 2.0 29.9% noncoding (1/1221 nt) IS30 repeat region
?NC_000913 = 1995730 68 (0.750)coding (76/177 nt) yecU protein YecU
* ? NC_000913 = 174349957 (0.620)30 (0.330) 24/590 2.4 34.5% coding (43/1374 nt) mdtK multidrug efflux pump MdtK
?NC_000913 2101749 = NA (NA)noncoding (1195/1195 nt) IS5 repeat region
* ? NC_000913 1979271 =0 (0.000)98 (1.070) 66/590 0.1 100% intergenic (‑56/‑482) insA5/uspC IS1 family protein InsA/universal stress protein C
?NC_000913 = 2102947 NA (NA)pseudogene (443/446 nt) wbbL interrupted rhamnosyltransferase WbbL
* ? NC_000913 1995507 =92 (1.010)27 (0.290) 21/590 2.9 22.7% intergenic (‑148/‑148) uvrY/yecU DNA‑binding transcriptional activator UvrY/protein YecU
?NC_000913 2170171 = NA (NA)noncoding (1/1258 nt) IS3 repeat region
* ? NC_000913 = 199550992 (1.010)32 (0.350) 28/590 1.9 25.8% intergenic (‑150/‑146) uvrY/yecU DNA‑binding transcriptional activator UvrY/protein YecU
?NC_000913 = 2171428 NA (NA)noncoding (1258/1258 nt) IS3 repeat region
* ? NC_000913 = 230574041 (0.450)44 (0.490) 35/578 1.2 55.3% coding (1015/1647 nt) mqo malate:quinone oxidoreductase
?NC_000913 2306377 = 31 (0.350)coding (378/1647 nt) mqo malate:quinone oxidoreductase
* ? NC_000913 3203595 =105 (1.150)32 (0.360) 25/578 2.2 27.0% coding (537/822 nt) bacA undecaprenyl pyrophosphate phosphatase
?NC_000913 = 3281168 70 (0.780)intergenic (+478/‑808) agaV/agaS N‑acetyl‑D‑galactosamine specific PTS enzyme IIB component/putative galactosamine‑6‑phosphate deaminase/isomerase
* ? NC_000913 = 353342747 (0.510)41 (0.460) 30/570 1.6 47.0% coding (610/1623 nt) pck phosphoenolpyruvate carboxykinase (ATP)
?NC_000913 3533620 = 47 (0.530)coding (803/1623 nt) pck phosphoenolpyruvate carboxykinase (ATP)
* ? NC_000913 = 419052166 (0.720)36 (0.400) 32/576 1.4 37.4% intergenic (‑34/+214) sroH/thiH small RNA SroH/2‑iminoacetate synthase
?NC_000913 4190728 = 56 (0.630)intergenic (‑241/+7) sroH/thiH small RNA SroH/2‑iminoacetate synthase