breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 278,744 +A intergenic (‑239/+75) PP_0224 ← / ← sctC DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein
RA 307,866 +C intergenic (+881/‑988) hslO → / → PP_0254 molecular chaperone HslO/hypothetical protein
RA 336,125 +T coding (210/237 nt) PP_0278 → hypothetical protein
RA 353,067 A→G intergenic (+34/+84) hisF → / ← cbcV imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein
RA 499,203 A→G intergenic (+47/‑249) uhpA → / → PP_0411 two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein
RA 1,070,248 +GA intergenic (+48/+94) aroP‑I → / ← PP_0928 aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
RA 1,126,647 +C intergenic (‑101/+48) tdcG‑II ← / ← gcvP‑I L‑serine dehydratase/glycine dehydrogenase
RA 1,419,549 +C intergenic (‑38/+98) PP_1242 ← / ← PP_1244 hypothetical protein/hypothetical protein
RA 1,499,480 2 bp→AC intergenic (+57/‑106) trpS → / → zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
RA 1,499,498 1 bp→CG intergenic (+75/‑89) trpS → / → zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
RA 1,499,508 +C intergenic (+85/‑79) trpS → / → zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
RA 1,932,640 +C intergenic (‑107/+43) rluA ← / ← minE bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor
RA 2,921,460 G→A G3494R (GGG→AGG)  PP_2561 → hemolysin‑type calcium‑binding bacteriocin
RA 3,845,705 +G intergenic (‑72/+26) PP_3394 ← / ← PP_3395 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator
RA 3,951,159 T→C intergenic (‑123/+72) PP_3486 ← / ← PP_3487 cytochrome c/hypothetical protein
RA 3,951,161 A→T intergenic (‑125/+70) PP_3486 ← / ← PP_3487 cytochrome c/hypothetical protein
RA 4,586,030 2 bp→TC intergenic (+113/+101) PP_4061 → / ← PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
RA 4,586,035 +G intergenic (+118/+97) PP_4061 → / ← PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
RA 4,586,057 +C intergenic (+140/+75) PP_4061 → / ← PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
RA 4,635,709 C→T G16D (GGT→GAT)  uvrY ← BarA/UvrY two‑componenent system response regulator
RA 4,733,447 A→G Y730H (TAT→CAT)  sucA ← 2‑oxoglutarate dehydrogenase subunit E1
RA 4,740,811 (T)7→6 intergenic (+48/+705) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,740,816 T→G intergenic (+53/+700) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,740,819 2 bp→CT intergenic (+56/+696) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,229 A→C intergenic (+466/+287) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,231 C→G intergenic (+468/+285) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,234 C→T intergenic (+471/+282) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,236 2 bp→TG intergenic (+473/+279) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,239 A→G intergenic (+476/+277) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,243 3 bp→TGC intergenic (+480/+271) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,255 C→T intergenic (+492/+261) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,257 A→C intergenic (+494/+259) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,260 2 bp→GC intergenic (+497/+255) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,263 A→C intergenic (+500/+253) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,272 A→G intergenic (+509/+244) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,274 A→C intergenic (+511/+242) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,276 G→C intergenic (+513/+240) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,278 C→T intergenic (+515/+238) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,283 +T intergenic (+520/+233) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,289 C→G intergenic (+526/+227) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,292 C→T intergenic (+529/+224) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,294 C→G intergenic (+531/+222) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,296 A→C intergenic (+533/+220) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,741,298 C→T intergenic (+535/+218) gltA → / ← yeiW citrate synthase/putative oxidoreductase
JC 4,980,585 +GGC intergenic (‑24/+44) PP_4387 ← / ← flgE hypothetical protein/flagellar hook protein FlgE
JC 5,555,608 +GCC intergenic (‑84/+87) PP_4887 ← / ← PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
RA 5,674,751 +G intergenic (+113/+27) rhlE‑II → / ← yceI ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor
RA 5,674,753 G→C intergenic (+115/+25) rhlE‑II → / ← yceI ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor
JC 5,681,415 +CGGG intergenic (‑133/+71) PP_4986 ← / ← PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
RA 5,948,277 C→T R66H (CGT→CAT)  rho ← transcription termination factor Rho
RA 6,013,885 T→C intergenic (+90/+20) xpt → / ← PP_5266 xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_002947 55549 55610 62 2 [1] [1] 3 PP_5423 membrane protein
* * ÷ NC_002947 171377–172964 176273–172979 16–4897 2 [1] [0] 2 PP_16SA–[PP_5SA] PP_16SA,PP_23SA,[PP_5SA]
* * ÷ NC_002947 176681–178394 181681–178409 16–5001 2 [1] [1] 3 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]
* * ÷ NC_002947 1180094 1180169 76 2 [1] [1] 2 PP_1033 sulfatase domain‑containing protein
* * ÷ NC_002947 1370683 1370719 37 3 [1] [0] 2 PP_1195 hypothetical protein
* * ÷ NC_002947 2005743 2005800 58 2 [1] [1] 2 PP_1788/PP_1789 hypothetical protein/haloacid dehalogenase‑like family hydrolase
* * ÷ NC_002947 2087939 2088036 98 2 [1] [1] 3 PP_1865/aroH transposase/3‑deoxy‑7‑phosphoheptulonate synthase
* * ÷ NC_002947 2109471 2109534 64 4 [1] [0] 2 PP_1882 membrane protein
* * ÷ NC_002947 2182469 2182555 87 2 [1] [1] 2 PP_5487 hypothetical protein
* * ÷ NC_002947 2185201 2185334 134 2 [1] [1] 2 PP_1936 membrane protein
* * ÷ NC_002947 2599424 2599512 89 2 [0] [1] 2 PP_2277 hypothetical protein
* * ÷ NC_002947 2837046 2837179 134 2 [1] [1] 2 [sad‑I] [sad‑I]
* * ÷ NC_002947 3382852 3382876 25 2 [0] [1] 2 PP_5545/PP_5546 hypothetical protein/hypothetical protein
* * ÷ NC_002947 3411408 3411509 102 2 [1] [1] 3 [PP_5550]–[PP_5551] [PP_5550],[PP_5551]
* * ÷ NC_002947 3517331 3517413 83 2 [1] [1] 3 PP_5578 hypothetical protein
* * ÷ NC_002947 3520268 3520360 93 2 [1] [1] 2 PP_5582 hypothetical protein
* * ÷ NC_002947 3521321 3521418 98 2 [1] [1] 2 PP_5582/PP_5583 hypothetical protein/hypothetical protein
* * ÷ NC_002947 3578813 3578839 27 3 [1] [1] 2 PP_5589 rhs repeat‑associated core domain‑containing protein
* * ÷ NC_002947 3733549 3734281 733 16 [0] [1] 2 [PP_3300]–[PP_3301] [PP_3300],[PP_3301]
* * ÷ NC_002947 3734487 3736072 1586 2 [1] [0] 2 [PP_3301]–[PP_3302] [PP_3301],[PP_3302]
* * ÷ NC_002947 3736210 3739457 3248 2 [0] [1] 2 [PP_3302]–[PP_3303] [PP_3302],[PP_3303]
* * ÷ NC_002947 3739502 3743303 3802 2 [1] [1] 2 [PP_3303]–[paoA] [PP_3303],PP_3304,PP_3305,PP_3306,PP_3307,[paoA]
* * ÷ NC_002947 3743306 3744589 1284 2 [1] [1] 2 [paoA]–[paoB] [paoA],[paoB]
* * ÷ NC_002947 3744737 3744906 170 2 [1] [1] 2 paoC aromatic aldehyde dehydrogenase molybdopterin‑binding subunit
* * ÷ NC_002947 3745039 3751112 6074 2 [1] [1] 2 [paoC]–[PP_3316] [paoC],kefB‑II,PP_3312,PP_3313,PP_3314,PP_3315,[PP_3316]
* * ÷ NC_002947 3751224 3752275 1052 2 [1] [1] 2 PP_3316 chaperone‑associated ATPase
* * ÷ NC_002947 3752422 3752752 331 2 [1] [1] 2 PP_3316 chaperone‑associated ATPase
* * ÷ NC_002947 3752855 3753313 459 2 [1] [1] 2 PP_3316 chaperone‑associated ATPase
* * ÷ NC_002947 3753426 3754781 1356 2 [1] [1] 2 [PP_3316]–[PP_3319] [PP_3316],PP_3317,PP_3318,[PP_3319]
* * ÷ NC_002947 3754850 3756211 1362 2 [1] [1] 2 PP_3319 GGDEF domain‑containing sensory box protein
* * ÷ NC_002947 3756338 3757179 842 2 [1] [1] 2 [PP_3319]–[PP_3321] [PP_3319],PP_3320,[PP_3321]
* * ÷ NC_002947 3757200 3759561 2362 2 [1] [1] 2 [PP_3321]–[folEB] [PP_3321],hemBB,PP_3323,[folEB]
* * ÷ NC_002947 3759721 3759976 256 2 [1] [1] 2 folEB GTP cyclohydrolase I
* * ÷ NC_002947 3760061 3761145 1085 2 [1] [0] 2 [folEB]–[PP_3325] [folEB],[PP_3325]
* * ÷ NC_002947 3761374 3761938 565 2 [1] [1] 2 PP_3325 ferric siderophore receptor
* * ÷ NC_002947 3762034 3764933 2900 2 [1] [1] 2 [PP_3325]–PP_3326 [PP_3325],PP_3326
* * ÷ NC_002947 3765008 3767079 2072 2 [1] [1] 2 PP_3328–[PP_3329] PP_3328,PP_5599,[PP_3329]
* * ÷ NC_002947 3767098 3767872 775 2 [1] [1] 2 [PP_3329] [PP_3329]
* * ÷ NC_002947 3767918 3768138 221 2 [1] [0] 2 [PP_5600] [PP_5600]
* * ÷ NC_002947 3768404 3768836 433 2 [1] [1] 2 [PP_3330] [PP_3330]
* * ÷ NC_002947 3768848 3769188 341 2 [1] [1] 2 PP_3330 ferric siderophore receptor
* * ÷ NC_002947 3769473 3772051 2579 2 [1] [0] 2 [PP_3330]–[PP_3331] [PP_3330],[PP_3331]
* * ÷ NC_002947 3772175 3773550 1376 3 [1] [1] 2 PP_3332–[PP_5743] PP_3332,PP_3333,[PP_5743]
* * ÷ NC_002947 3773585 3773892 308 2 [1] [1] 2 PP_5743 TonB‑dependent receptor protein
* * ÷ NC_002947 3774035 3774738 704 2 [1] [1] 2 [PP_5743]–[PP_3335] [PP_5743],[PP_3335]
* * ÷ NC_002947 3774999 3775120 122 2 [1] [1] 2 [PP_3336] [PP_3336]
* * ÷ NC_002947 3775330 3776527 1198 3 [1] [1] 2 [PP_3336]–[PP_3339] [PP_3336],PP_3337,PP_3338,[PP_3339]
* * ÷ NC_002947 3776565 3777201 637 2 [1] [1] 2 [PP_3339]–[PP_3340] [PP_3339],[PP_3340]
* * ÷ NC_002947 3777465 3778509 1045 2 [1] [0] 2 PP_3340 TonB‑dependent receptor
* * ÷ NC_002947 3778635 3779485 851 2 [0] [1] 2 [PP_3340]–nikR [PP_3340],nikR
* * ÷ NC_002947 3779614 3779705 92 2 [1] [1] 2 nikA nickel ABC transporter substrate‑binding protein
* * ÷ NC_002947 3779798 3780143 346 2 [1] [1] 2 nikA nickel ABC transporter substrate‑binding protein
* * ÷ NC_002947 3780189 3781558 1370 2 [1] [0] 2 [nikA]–[nikB] [nikA],[nikB]
* * ÷ NC_002947 3781707 3784045 2339 2 [1] [1] 2 [nikB]–[nikE] [nikB],nikC,nikD,[nikE]
* * ÷ NC_002947 3784118 3785940 1823 2 [1] [1] 2 [nikE]–[PP_3348] [nikE],[PP_3348]
* * ÷ NC_002947 3786029 3787705 1677 2 [1] [0] 2 [mhpT]–[PP_3350] [mhpT],[PP_3350]
* * ÷ NC_002947 3787834 3788578 745 2 [0] [1] 2 PP_3350 hypothetical protein
* * ÷ NC_002947 3788625 3790412 1788 2 [1] [1] 2 [PP_3350]–[atsA] [PP_3350],[atsA]
* * ÷ NC_002947 3790551 3790893 343 2 [1] [1] 2 [atsA]–[PP_3353] [atsA],[PP_3353]
* * ÷ NC_002947 3791339 3793332 1994 2 [1] [0] 16 [PP_3353]–[PP_3355] [PP_3353],PP_3354,[PP_3355]
* * ÷ NC_002947 4195165 4195318 154 3 [1] [1] 2 PP_3688 hypothetical protein
* * ÷ NC_002947 4232624 4232643 20 2 [1] [1] 3 PP_3710 hypothetical protein
* * ÷ NC_002947 4373414 4373445 32 3 [1] [1] 2 PP_3849 hemolysin‑type calcium‑binding protein
* * ÷ NC_002947 4376687 4376743 57 2 [1] [1] 2 PP_3852 BNR domain‑containing protein
* * ÷ NC_002947 4619128 4619582 455 3 [1] [1] 2 PP_5652/PP_5654 hypothetical protein/phosphotriesterase
* * ÷ NC_002947 4624212 4624357 146 2 [1] [1] 3 PP_5654/PP_4091 phosphotriesterase/transposase
* * ÷ NC_002947 4628394 4628517 124 2 [1] [1] 2 PP_4092/PP_5655 transposase/hypothetical protein
* * ÷ NC_002947 4808163 4808235 73 4 [1] [1] 2 PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* * ÷ NC_002947 5004572 5004642 71 2 [1] [0] 2 PP_4410 hypothetical protein
* * ÷ NC_002947 5042356 5042450 95 2 [0] [1] 2 PP_4447 hypothetical protein
* * ÷ NC_002947 5068711 5068815 105 2 [1] [1] 3 PP_4465 porin
* * ÷ NC_002947 5603508 5603606 99 3 [1] [1] 2 PP_4925 hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 = 149945835 (0.720)9 (0.190) 8/280 1.1 24.8% intergenic (+35/‑129) trpS/zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
?NC_002947 = 1499495 20 (0.420)intergenic (+72/‑92) trpS/zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
* ? NC_002947 2301453 =0 (0.000)38 (0.800) 22/278 0.5 100% intergenic (‑97/‑234) sbcD/PP_5497 exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein
?NC_002947 2925429 = NA (NA)intergenic (‑177/+388) PP_2563/PP_2564 antibiotic biosynthesis protein/quercetin 2,3‑dioxygenase
* ? NC_002947 = 23014540 (0.000)16 (0.330) 16/280 0.7 100% intergenic (‑98/‑233) sbcD/PP_5497 exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein
?NC_002947 5545321 = NA (NA)intergenic (‑461/+416) rpsF/rlmB 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB
* ? NC_002947 = 37335480 (0.000)16 (0.330) 16/284 0.7 100% coding (237/615 nt) PP_3300 Transcriptional regulator, tetR family
?NC_002947 3793333 = 0 (0.000)coding (1190/1191 nt) PP_3355 beta‑ketothiolase
* ? NC_002947 5545321 =NA (NA)21 (0.440) 21/280 0.5 100% intergenic (‑461/+416) rpsF/rlmB 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB
?NC_002947 = 5621245 0 (0.000)coding (19/774 nt) PP_4939 hypothetical protein
* ? NC_002947 = 5545666NA (NA)14 (0.290) 12/278 0.9 100% intergenic (‑806/+71) rpsF/rlmB 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB
?NC_002947 5621244 = 0 (0.000)coding (20/774 nt) PP_4939 hypothetical protein