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 226,969 G→A noncoding (360/1542 nt) ECD_RS01035 → 16S ribosomal RNA
RA 405,802 G→T T234K (ACG→AAG)  ispA ← (2E,6E)‑farnesyl diphosphate synthase
RA 519,071 G→A T100T (ACG→ACA)  ylbF → DUF2877 domain‑containing protein
RA 537,641 G→A G49R (GGA→AGA)  ybcK → recombinase family protein
RA 550,559 C→A pseudogene (10/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,561 G→A pseudogene (12/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,564 T→C pseudogene (15/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,663 G→A pseudogene (114/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,708 T→C pseudogene (159/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,712 C→T pseudogene (163/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,798 A→T pseudogene (249/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,888 G→A pseudogene (339/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,900 C→T pseudogene (351/364 nt) ECD_RS02680 → prophage tail fiber N‑terminal domain‑containing protein
RA 550,927 G→A intergenic (+14/+71) ECD_RS02680 → / ← ECD_RS02685 prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein
RA 550,939 C→A intergenic (+26/+59) ECD_RS02680 → / ← ECD_RS02685 prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein
RA 550,945 T→A intergenic (+32/+53) ECD_RS02680 → / ← ECD_RS02685 prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein
RA 550,988 A→C intergenic (+75/+10) ECD_RS02680 → / ← ECD_RS02685 prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein
RA 642,526 A→T K5* (AAA→TAA)  ECD_RS25105 → IS3‑like element IS150 family transposase
MC JC 748,650 Δ4,449 bp lacI–[ECD_RS03715] lacI, ECD_RS03705, ECD_RS03710, [ECD_RS03715]
RA 753,173 G→A pseudogene (831/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 753,248 T→C pseudogene (756/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 753,262 T→C pseudogene (742/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 753,271 C→T pseudogene (733/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 753,513 T→G pseudogene (491/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 753,674 A→C pseudogene (330/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 753,778 A→G pseudogene (226/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 753,860 A→G pseudogene (144/921 nt) ECD_RS03715 ← phage integrase Arm DNA‑binding domain‑containing protein
RA 754,025 C→T G59S (GGC→AGC)  ECD_RS03720 ← excisionase
RA 754,080 C→T E40E (GAG→GAA)  ECD_RS03720 ← excisionase
RA 754,104 T→A P32P (CCA→CCT)  ECD_RS03720 ← excisionase
RA 754,122 C→G R26R (CGG→CGC)  ECD_RS03720 ← excisionase
RA 754,125 A→C V25V (GTT→GTG)  ECD_RS03720 ← excisionase
RA 754,158 A→G R14R (CGT→CGC)  ECD_RS03720 ← excisionase
RA 754,170 T→A A10A (GCA→GCT)  ECD_RS03720 ← excisionase
RA 754,247 C→A A54S (GCC→TCC)  ECD_RS03725 ← hypothetical protein
RA 754,286 C→T V41I (GTA→ATA)  ECD_RS03725 ← hypothetical protein
RA 754,371 C→T E12E (GAG→GAA)  ECD_RS03725 ← hypothetical protein
RA 754,386 T→A G7G (GGA→GGT)  ECD_RS03725 ← hypothetical protein
RA 762,867 T→G L169L (CTT→CTG)  ECD_RS03820 → replication protein P
RA 762,873 T→C D171D (GAT→GAC)  ECD_RS03820 → replication protein P
RA 762,885 C→G R175R (CGC→CGG)  ECD_RS03820 → replication protein P
RA 762,888 T→C R176R (CGT→CGC)  ECD_RS03820 → replication protein P
RA 762,894 C→T A178A (GCC→GCT)  ECD_RS03820 → replication protein P
RA 762,897 A→C A179A (GCA→GCC)  ECD_RS03820 → replication protein P
RA 762,903 G→A E181E (GAG→GAA)  ECD_RS03820 → replication protein P
RA 762,906 Δ1 bp coding (546/702 nt) ECD_RS03820 → replication protein P
RA 762,911 1 bp→TG coding (551/702 nt) ECD_RS03820 → replication protein P
RA 762,918 T→C T186T (ACT→ACC)  ECD_RS03820 → replication protein P
RA 762,922 A→C R188R (AGA→CGA)  ECD_RS03820 → replication protein P
RA 762,945 C→A I195I (ATC→ATA)  ECD_RS03820 → replication protein P
RA 763,051 G→T A231S (GCA→TCA)  ECD_RS03820 → replication protein P
RA 763,103 T→G intergenic (+41/‑73) ECD_RS03820 → / → ECD_RS03830 replication protein P/metallophosphoesterase
RA 763,115 G→A intergenic (+53/‑61) ECD_RS03820 → / → ECD_RS03830 replication protein P/metallophosphoesterase
RA 763,117 C→A intergenic (+55/‑59) ECD_RS03820 → / → ECD_RS03830 replication protein P/metallophosphoesterase
RA 763,131 C→G intergenic (+69/‑45) ECD_RS03820 → / → ECD_RS03830 replication protein P/metallophosphoesterase
RA 763,139 C→T intergenic (+77/‑37) ECD_RS03820 → / → ECD_RS03830 replication protein P/metallophosphoesterase
RA 763,145 A→C intergenic (+83/‑31) ECD_RS03820 → / → ECD_RS03830 replication protein P/metallophosphoesterase
RA 763,166 C→T intergenic (+104/‑10) ECD_RS03820 → / → ECD_RS03830 replication protein P/metallophosphoesterase
RA 763,181 A→G A2A (GCA→GCG)  ECD_RS03830 → metallophosphoesterase
RA 763,190 2 bp→AA coding (15‑16/687 nt) ECD_RS03830 → metallophosphoesterase
RA 763,193 T→C L6L (CTT→CTC)  ECD_RS03830 → metallophosphoesterase
RA 763,199 2 bp→CG coding (24‑25/687 nt) ECD_RS03830 → metallophosphoesterase
RA 763,202 C→T I9I (ATC→ATT)  ECD_RS03830 → metallophosphoesterase
RA 763,205 A→T E10D (GAA→GAT)  ECD_RS03830 → metallophosphoesterase
RA 767,828 A→C K40Q (AAG→CAA)  ybcW → protein YbcW
RA 767,830 G→A K40Q (AAG→CAA)  ybcW → protein YbcW
RA 767,851 A→G R47R (AGA→AGG)  ybcW → protein YbcW
RA 767,863 A→C A51A (GCA→GCC)  ybcW → protein YbcW
RA 767,869 G→A L53L (TTG→TTA)  ybcW → protein YbcW
RA 767,872 G→A V54V (GTG→GTA)  ybcW → protein YbcW
RA 767,884 T→G N58K (AAT→AAG)  ybcW → protein YbcW
RA 767,889 T→C M60T (ATG→ACG)  ybcW → protein YbcW
RA 767,934 T→C intergenic (+17/+148) ybcW → / ← ECD_RS03870 protein YbcW/YlcI/YnfO family protein
RA 788,122 A→G intergenic (+62/‑3) lom → / → ECD_RS23105 outer membrane beta‑barrel protein Lom/prophage tail fiber N‑terminal domain‑containing protein
RA 791,198 C→T intergenic (‑628/+228) ECD_RS03990 ← / ← ybhB hypothetical protein/kinase inhibitor
RA 791,250 A→T intergenic (‑680/+176) ECD_RS03990 ← / ← ybhB hypothetical protein/kinase inhibitor
RA 855,155 G→A E90E (GAG→GAA)  gsiC → glutathione ABC transporter permease GsiC
RA 862,724 T→C S22P (TCT→CCT)  yliI → aldose sugar dehydrogenase YliI
RA 931,389 G→T S37S (TCC→TCA)  infA ← translation initiation factor IF‑1
RA 992,215 C→T intergenic (‑143/+459) ompF ← / ← asnS porin OmpF/asparagine‑‑tRNA ligase
RA 1,002,731 G→A intergenic (‑130/‑226) ssuE ← / → elfA NADPH‑dependent FMN reductase/fimbrial protein
RA 1,026,045 A→G intergenic (‑37/‑182) sulA ← / → sxy SOS‑induced cell division inhibitor SulA/CRP‑S regulon transcriptional coactivator Sxy
RA 1,100,143 G→A noncoding (76/88 nt) ECD_RS05485 ← tRNA‑Ser
RA 1,137,851 A→C S186R (AGC→CGC)  flgG → flagellar basal‑body rod protein FlgG
RA 1,173,770 G→A L930F (CTT→TTT)  mfd ← transcription‑repair coupling factor
RA 1,308,529 G→A Q4* (CAA→TAA)  trpE ← anthranilate synthase component I
RA 1,384,274 A→G pseudogene (421/753 nt) fnr ← fumarate/nitrate reduction transcriptional regulator Fnr
RA 1,814,885 C→T L42F (CTC→TTC)  cdgI → GGDEF domain‑containing protein
RA 1,822,910 A→C R273R (CGA→CGC)  dgcP → diguanylate cyclase DgcP
RA 1,834,871 G→A P201L (CCC→CTC)  fadD ← long‑chain‑fatty‑acid‑‑CoA ligase FadD
RA 1,949,161 T→G W122G (TGG→GGG)  mtfA → DgsA anti‑repressor MtfA
RA 1,973,596 T→C pseudogene (4/699 nt)
pseudogene (144/144 nt)		 ECD_RS10050 ←
ECD_RS25675 ←		 IS3‑like element IS2 family transposase
putative zinc ribbon protein
RA 2,007,879 A→T I247N (ATT→AAT)  wzx ← O7 family O‑antigen flippase
MC JC 2,068,532 Δ776 bp ECD_RS10480–[ECD_RS10485] ECD_RS10480, ECD_RS10480, [ECD_RS10485]
RA 2,075,017 A→C intergenic (‑10/+290) gatY ← / ← fbaB tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase
JC 2,135,130 +GACAT pseudogene (118/994 nt) mglB ← galactose/glucose ABC transporter substrate‑binding protein MglB
RA 2,227,497 2 bp→AA coding (2284‑2285/2628 nt) gyrA ← DNA topoisomerase (ATP‑hydrolyzing) subunit A
RA 2,275,119 2 bp→TG intergenic (+4/‑98) ECD_RS25720 → / → yfbM hypothetical protein/YfbM family protein
RA 2,373,775 C→T N82N (AAC→AAT)  lpxP → kdo(2)‑lipid IV(A) palmitoleoyltransferase
RA 2,413,824 G→A L87L (CTG→TTG)  cysW ← sulfate/thiosulfate ABC transporter permease CysW
RA 2,477,975 T→C F532S (TTC→TCC)  hyfR → DNA‑binding transcriptional regulator HyfR
MC JC 2,517,851 Δ1,445 bp ECD_RS25300–ECD_RS25300 ECD_RS25300, ECD_RS25300
RA 2,567,019 C→T intergenic (‑223/+198) shoB ← / ← acpS type I toxin‑antitoxin system toxin ShoB/holo‑ACP synthase
RA 2,764,352 C→T T236T (ACC→ACT)  xni → flap endonuclease Xni
MC JC 2,820,977 Δ1,446 bp [ECD_RS14045]–[ECD_RS14060] [ECD_RS14045], ECD_RS25310, ECD_RS25310, [ECD_RS14060]
RA 2,879,376 C→A V175V (GTG→GTT)  gcvP ← aminomethyl‑transferring glycine dehydrogenase
RA 2,880,243 C→T D56N (GAT→AAT)  gcvH ← glycine cleavage system protein GcvH
RA 2,880,800 T→C T243A (ACC→GCC)  gcvT ← glycine cleavage system aminomethyltransferase GcvT
RA 2,891,803 G→A G32G (GGG→GGA)  scpA → methylmalonyl‑CoA mutase
RA 2,891,814 A→C K36T (AAG→ACG)  scpA → methylmalonyl‑CoA mutase
MC JC 2,969,387 Δ670 bp coding (226‑895/1494 nt) gspE ← type II secretion system ATPase GspE
RA 3,162,393 C→T L165L (CTC→CTT)  lpoA → penicillin‑binding protein activator LpoA
RA 3,197,975 2 bp→GT coding (514‑515/1434 nt) dacB → serine‑type D‑Ala‑D‑Ala carboxypeptidase
RA 3,443,292 G→A A221A (GCC→GCT)  yhhX ← oxidoreductase
RA 3,496,959 C→T intergenic (‑116/‑267) ECD_RS17420 ← / → yhiM YhiJ/YhiL family protein/DUF2776 domain‑containing protein
RA 3,733,869 T→G H513Q (CAT→CAG)  adeD → adenine deaminase
RA 3,757,620 G→A L151L (CTC→CTT)  yidR ← DUF3748 domain‑containing protein
RA 3,817,054 T→C M451V (ATG→GTG)  viaA ← ATPase RavA stimulator ViaA
MC JC 3,822,341 Δ1,441 bp [rbsD]–[rbsD] [rbsD], ECD_RS25390, ECD_RS25390, [rbsD]
RA 3,997,577 A→G F459F (TTT→TTC)  frvB ← PTS fructose‑like transporter subunit IIBC
RA 4,072,111 T→C pseudogene (172/1845 nt) btuB → TonB‑dependent vitamin B12 receptor BtuB
RA 4,108,278 C→T intergenic (+132/‑55) yjaG → / → hupA YjaG family protein/nucleoid‑associated protein HU‑alpha
RA 4,179,097 Δ1 bp coding (2184/2823 nt) uvrA ← excinuclease ABC subunit UvrA
RA 4,181,483 C→T intergenic (‑203/‑52) uvrA ← / → ssb1 excinuclease ABC subunit UvrA/single‑stranded DNA‑binding protein SSB1
JC 4,302,992 (GCC)2→1 coding (408‑410/1338 nt) amiB → N‑acetylmuramoyl‑L‑alanine amidase AmiB
RA 4,395,355 G→T T108T (ACC→ACA)  holC ← DNA polymerase III subunit chi

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_012971 543877–544405 549187 4783–5311 33 [32] [0] 121 [ECD_RS02625]–[ECD_RS02675] [ECD_RS02625],ECD_RS02625,ECD_RS02630,essD,rrrD,rzpD,iss,ECD_RS02660,ECD_RS02670,[ECD_RS02675]
* * ÷ NC_012971 550423 550552 130 33 [32] [0] 53 [ECD_RS02675]–[ECD_RS02680] [ECD_RS02675],[ECD_RS02680]
* * ÷ NC_012971 550998 597471–596896 45899–46474 130 [0] [32] 35 [ECD_RS02685]–[ECD_RS02890] [ECD_RS02685],cusS,cusR,cusC,cusF,cusB,cusA,pheP,ybdG,nfsB,ybdF,ybdJ,ybdK,ECD_RS25095,ECD_RS22975,ECD_RS22975,ECD_RS24565,hokE,ECD_RS02775,entD,fepA,fes,ybdZ,entF,wzz(fepE),fepC,fepG,fepD,entS,fepB,entC,entE,entB,entA,entH,cstA,ybdD,hcxA,ybdL,ybdM,ECD_RS02885,ECD_RS02890,[ECD_RS02890]
* * ÷ NC_012971 754416 762860 8445 33 [32] [10] 118 ECD_RS03730–[ECD_RS03820] ECD_RS03730,ECD_RS26520,ECD_RS03740,ECD_RS26465,ECD_RS03750,ECD_RS03755,ECD_RS03760,bet,ECD_RS03770,kil,ECD_RS25555,ECD_RS03785,ECD_RS03790,ECD_RS03795,ECD_RS03800,ECD_RS03805,ECD_RS03810,ECD_RS24605,[ECD_RS03820]
* * ÷ NC_012971 763233 767816 4584 40 [31] [32] 36 [ECD_RS03830]–[ybcW] [ECD_RS03830],ECD_RS03835,ECD_RS03840,ECD_RS03845,rzpD,bor,ybcV,[ybcW]
* * ÷ NC_012971 767940 788118 20179 86 [0] [32] 33 ECD_RS03870–lom ECD_RS03870,ECD_RS03875,ECD_RS03880,ECD_RS03885,ECD_RS03890,ECD_RS03895,ECD_RS03900,ECD_RS03905,ECD_RS03910,ECD_RS03915,ECD_RS03920,ECD_RS03925,ECD_RS03930,gpG,ECD_RS03940,ECD_RS03945,ECD_RS03950,ECD_RS03955,ECD_RS03960,ECD_RS03965,gpJ,lom
* * ÷ NC_012971 788131 791178 3048 53 [0] [31] 34 [ECD_RS23105]–ECD_RS03990 [ECD_RS23105],ECD_RS03990
* * ÷ NC_012971 1586962 1588051–1586963 2–1090 129 [0] [32] 35 [ECD_RS26210]–[ECD_RS08025] [ECD_RS26210],ECD_RS08025,[ECD_RS08025]
* * ÷ NC_012971 2943444 2963014 19571 33 [32] [32] 33 [ECD_RS26060]–[yghD] [ECD_RS26060],ECD_RS23830,ECD_RS14635,ECD_RS14640,ECD_RS14645,ECD_RS14650,ECD_RS14655,kdsB,ECD_RS14665,ECD_RS14670,ECD_RS14675,ECD_RS14680,ECD_RS14685,ECD_RS14690,ECD_RS14690,ECD_RS14695,ECD_RS14700,ECD_RS14705,ECD_RS14710,[yghD]
* * ÷ NC_012971 3628812 3628930 119 34 [32] [32] 33 ECD_RS18025 polymorphic toxin type 34 domain‑containing protein
* * ÷ NC_012971 3944669–3945804 3946333–3946238 435–1665 33 [32] [31] 34 ECD_RS19585 23S ribosomal RNA
* * ÷ NC_012971 4153661 4159658 5998 134 [0] [0] 80 [malE]–ECD_RS20580 [malE],malK,lamB,malM,ECD_RS20580

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_012971 = 53661511 (0.110)108 (1.190) 56/556 0.2 94.6% pseudogene (1/228 nt) ECD_RS02560 protein ren
?NC_012971 762861 = 2 (0.020)coding (501/702 nt) ECD_RS03820 replication protein P
* ? NC_012971 549188 =0 (0.000)120 (1.250) 64/590 0.2 63.7% pseudogene (506/1809 nt) ECD_RS02675 phage tail tip protein
?NC_012971 2827816 = 137 (1.420)coding (552/570 nt) ECD_RS14080 hypothetical protein
* ? NC_012971 550553 =0 (0.000)53 (0.550) 28/588 2.2 100% pseudogene (4/364 nt) ECD_RS02680 prophage tail fiber N‑terminal domain‑containing protein
?NC_012971 = 788130 0 (0.000)pseudogene (6/1155 nt) ECD_RS23105 prophage tail fiber N‑terminal domain‑containing protein
* ? NC_012971 = 5509970 (0.000)129 (1.350) 71/586 0.1 100% intergenic (+84/+1) ECD_RS02680/ECD_RS02685 prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein
?NC_012971 = 1586961 0 (0.000)pseudogene (2/1929 nt) ECD_RS26210 phage head spike fiber domain‑containing protein
* ? NC_012971 = 7679390 (0.000)80 (1.250)
+99 bp		 45/392 0.1 100% intergenic (+22/+143) ybcW/ECD_RS03870 protein YbcW/YlcI/YnfO family protein
?NC_012971 = 1427848 NA (NA)pseudogene (3/522 nt) pdxI pyridoxine 4‑dehydrogenase
* ? NC_012971 = 3365925NA (NA)134 (1.390) 76/590 0.0 100% pseudogene (474/480 nt) ECD_RS16845 aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme
?NC_012971 = 4153660 0 (0.000)coding (132/1191 nt) malE maltose/maltodextrin ABC transporter substrate‑binding protein MalE
* ? NC_012971 = 348524699 (1.030)66 (1.080) 42/374 0.1 67.8% coding (3671/4236 nt) rhsB rhs element protein RhsB
?NC_012971 3628983 = 0 (0.000)coding (411/873 nt) ECD_RS18025 polymorphic toxin type 34 domain‑containing protein
* ? NC_012971 4159659 =0 (0.000)80 (0.830) 51/590 0.5 100% intergenic (+4/‑219) ECD_RS20580/ubiC SopA family protein/chorismate lyase
?NC_012971 4449936 = NA (NA)pseudogene (477/483 nt) fimB type 1 fimbria switch DNA invertase FimB
* ? NC_012971 = 44870900 (0.000)138 (1.470) 70/574 0.1 100% pseudogene (14/726 nt) ECD_RS22230 restriction endonuclease subunit S
?NC_012971 4487867 = 0 (0.000)intergenic (‑64/+69) ECD_RS22235/ECD_RS22240 IS1‑like element IS1A family transposase/restriction endonuclease subunit S