mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 277,149 | Δ1 bp | 10.0% | coding (546/1155 nt) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 495,361 | A→G | 17.4% | T23T (ACT→ACC) | aes ← | acetyl esterase |
| RA | 907,975 | G→T | 10.5% | A432A (GCC→GCA) | hcp ← | hybrid‑cluster [4Fe‑2S‑2O] protein in anaerobic terminal reductases |
| RA | 1,909,689 | T→C | 100% | K35E (AAA→GAA) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 2,116,551 | G→A | 21.0% | intergenic (‑91/+14) | cpsG ← / ← cpsB | phosphomannomutase/mannose‑1‑phosphate guanyltransferase |
| RA | 2,306,204 | G→A | 100% | L9L (CTG→TTG) | ompC ← | outer membrane porin protein C |
| RA | 3,207,739 | A→C | 100% | D445A (GAT→GCT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| JC | 3,270,623 | (CATTCAA)1→2 | 87.6% | coding (263/336 nt) | prlF → | antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,281,808 | T→C | 11.8% | D120D (GAT→GAC) | yraI → | putative periplasmic pilin chaperone |
| JC | 3,320,037 | Δ6 bp | 48.0% | coding (253‑258/1935 nt) | ftsH ← | protease, ATP‑dependent zinc‑metallo |
| RA | 3,528,377 | A→C | 100% | F284C (TTT→TGT) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,743,481 | G→T | 7.5% | A12A (GCG→GCT) | sgbE → | L‑ribulose‑5‑phosphate 4‑epimerase |
| RA | 4,368,787 | C→G | 100% | intergenic (‑26/+37) | ampC ← / ← frdD | penicillin‑binding protein; beta‑lactamase, intrinsically weak/fumarate reductase (anaerobic), membrane anchor subunit |
| RA | 4,589,705 | A→T | 7.6% | L101Q (CTG→CAG) | yjjA ← | putative DUF2501 family periplasmic protein |
| RA | 4,589,708 | A→T | 8.1% | V100E (GTG→GAG) | yjjA ← | putative DUF2501 family periplasmic protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 452046 | 452056 | 11 | 2 [1] | [1] 2 | tig/clpP | peptidyl‑prolyl cis/trans isomerase (trigger factor)/proteolytic subunit of ClpA‑ClpP and ClpX‑ClpP ATP‑dependent serine proteases |
| * | * | ÷ | CP009273 | 578955 | 579065 | 111 | 2 [1] | [1] 2 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | CP009273 | 651723 | 651735 | 13 | 3 [0] | [0] 3 | dcuC/pagP | anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase |
| * | * | ÷ | CP009273 | 716490 | 716510 | 21 | 2 [1] | [1] 2 | ybfK/kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | CP009273 | 950184 | 950204 | 21 | 2 [1] | [1] 2 | focA/ycaO | formate channel/ribosomal protein S12 methylthiotransferase accessory factor |
| * | * | ÷ | CP009273 | 1098845 | 1098916 | 72 | 2 [1] | [1] 2 | csgD/csgB | csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex |
| * | * | ÷ | CP009273 | 1207769 | 1207804 | 36 | 3 [1] | [1] 2 | iraM/ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| * | * | ÷ | CP009273 | 1211482 | 1211497 | 16 | 2 [1] | [1] 2 | ycgZ/ymgA | RcsB connector protein for regulation of biofilm and acid‑resistance/RcsB connector protein for regulation of biofilm |
| * | * | ÷ | CP009273 | 1566447 | 1566462 | 16 | 2 [1] | [1] 2 | gadB/pqqL | glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase |
| * | * | ÷ | CP009273 | 1573653 | 1573696 | 44 | 2 [1] | [1] 2 | yddA/ydeM | putative multidrug transporter subunit of ABC superfamily, membrane component/ATP‑binding component/putative YdeN‑specific sulfatase‑maturating enzyme |
| * | * | ÷ | CP009273 | 1577016 | 1577022 | 7 | 2 [1] | [1] 2 | ydeN/ydeO | putative Ser‑type periplasmic non‑aryl sulfatase/UV‑inducible global regulator, EvgA‑, GadE‑dependent |
| * | * | ÷ | CP009273 | 1631447 | 1631467 | 21 | 2 [1] | [1] 3 | ydfO | Qin prophage; uncharacterized protein |
| * | * | ÷ | CP009273 | 1631788 | 1631861 | 74 | 2 [1] | [1] 2 | ydfO/gnsB | Qin prophage; uncharacterized protein/Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts) |
| * | * | ÷ | CP009273 | 1662332 | 1662343 | 12 | 3 [1] | [1] 2 | mlc | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| * | * | ÷ | CP009273 | 1738074 | 1738099 | 26 | 2 [1] | [1] 2 | mdtK | multidrug efflux system transporter |
| * | * | ÷ | CP009273 | 1748921 | 1749020 | 100 | 2 [1] | [1] 2 | ydhY/ydhZ | putative 4Fe‑4S ferridoxin‑type protein; FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex/uncharacterized protein |
| * | * | ÷ | CP009273 | 1783817 | 1783853 | 37 | 2 [0] | [1] 2 | aroH/ydiE | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible/hemin uptake protein HemP homolog |
| * | * | ÷ | CP009273 | 1807102 | 1807136 | 35 | 2 [1] | [0] 2 | ydjO | uncharacterized protein |
| * | * | ÷ | CP009273 | 1807362 | 1807463 | 102 | 2 [1] | [1] 2 | [ydjO] | [ydjO] |
| * | * | ÷ | CP009273 | 1940395 | 1940438 | 44 | 2 [1] | [1] 2 | [yobI] | [yobI] |
| * | * | ÷ | CP009273 | 1952500 | 1952513 | 14 | 2 [1] | [1] 2 | torY/cutC | TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein |
| * | * | ÷ | CP009273 | 1973127 | 1973139 | 13 | 2 [1] | [1] 2 | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| * | * | ÷ | CP009273 | 2027362 | 2027454 | 93 | 2 [1] | [1] 2 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2050221 | 2050276 | 56 | 2 [1] | [1] 2 | amn/yeeN | AMP nucleosidase/UPF0082 family protein |
| * | * | ÷ | CP009273 | 2051130 | 2051154 | 25 | 2 [1] | [1] 3 | yeeN/asnW | UPF0082 family protein/tRNA‑Asn |
| * | * | ÷ | CP009273 | 2052502 | 2052549 | 48 | 2 [1] | [1] 2 | yeeO | putative multdrug exporter, MATE family |
| * | * | ÷ | CP009273 | 2185830 | 2185885 | 56 | 2 [1] | [1] 2 | yehD/yehE | putative fimbrial‑like adhesin protein/DUF2574 family protein |
| * | * | ÷ | CP009273 | 2379416 | 2379417 | 2 | 2 [0] | [0] 3 | yfbL | putative peptidase |
| * | * | ÷ | CP009273 | 2449114 | 2449154 | 41 | 2 [1] | [1] 2 | [yfcV] | [yfcV] |
| * | * | ÷ | CP009273 | 2461961 | 2461980 | 20 | 2 [1] | [1] 2 | gtrB | CPS‑53 (KpLE1) prophage; bactoprenol glucosyl transferase |
| * | * | ÷ | CP009273 | 2463005 | 2463026 | 22 | 2 [1] | [0] 2 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2463177 | 2463195 | 19 | 2 [0] | [1] 2 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2463563 | 2463603 | 41 | 3 [1] | [1] 2 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2466473 | 2466490 | 18 | 2 [1] | [1] 2 | oweS | pseudogene, CPS‑53 (KpLE1) prophage; bacteriophage replication protein O family;Phage or Prophage Related |
| * | * | ÷ | CP009273 | 2478801 | 2478806 | 6 | 2 [1] | [0] 2 | evgS | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| * | * | ÷ | CP009273 | 2481760 | 2481775 | 16 | 2 [1] | [0] 3 | yfdE | acetyl‑CoA:oxalate CoA‑transferase |
| * | * | ÷ | CP009273 | 2491962 | 2492013 | 52 | 2 [1] | [1] 2 | alaC/ypdA | valine‑pyruvate aminotransferase 3/sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system |
| * | * | ÷ | CP009273 | 2514437–2514449 | 2514449 | 1–13 | 2 [1] | [1] 2 | valU | tRNA‑Val |
| * | * | ÷ | CP009273 | 2741604 | 2741608 | 5 | 4 [0] | [1] 2 | ypjD | cytochrome c assembly protein family inner membrane protein |
| * | * | ÷ | CP009273 | 2768267 | 2768287 | 21 | 2 [1] | [1] 2 | yfjW | CP4‑57 prophage; putative inner membrane protein |
| * | * | ÷ | CP009273 | 2779823 | 2779883 | 61 | 2 [1] | [1] 2 | ygaQ | uncharacterized protein; putative enzyme |
| * | * | ÷ | CP009273 | 2982649 | 2982731 | 83 | 2 [1] | [1] 2 | [yqeI]–[yqeJ] | [yqeI],[yqeJ] |
| * | * | ÷ | CP009273 | 2986859 | 2986940 | 82 | 2 [0] | [1] 2 | ygeH/ygeI | putative transcriptional regulator/uncharacterized protein |
| * | * | ÷ | CP009273 | 2988506 | 2988633 | 128 | 2 [1] | [1] 2 | ygeK/ygeN | pseudogene; putative 2‑component transcriptional regulator/pseudogene |
| * | * | ÷ | CP009273 | 3378655 | 3378667 | 13 | 2 [1] | [1] 2 | argR/yhcN | l‑arginine‑responsive arginine metabolism regulon transcriptional regulator/cadmium and peroxide resistance protein, stress‑induced |
| * | * | ÷ | CP009273 | 3463355 | 3463420 | 66 | 2 [1] | [1] 2 | chiA/tufA | periplasmic endochitinase/translation elongation factor EF‑Tu 1 |
| * | * | ÷ | CP009273 | 3791546 | 3791600 | 55 | 2 [1] | [1] 2 | [waaL]–[waaU] | [waaL],[waaU] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 237781 | 38 (1.380) | 4 (0.150) | 3/260 | NT | 8.9% | coding (2010/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | CP009273 | = 238095 | 46 (1.760) | coding (1696/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | CP009273 | = 311124 | 3 (0.110) | 3 (0.120) | 3/248 | NT | 52.5% | coding (123/300 nt) | insE1 | IS3 transposase A |
| ? | CP009273 | = 311324 | NA (NA) | coding (27/867 nt) | insF1 | IS3 transposase B | |||||
| * | ? | CP009273 | 360104 = | 23 (0.830) | 48 (1.740) | 35/274 | NT | 63.6% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | 32 (1.160) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 1203246 = | 11 (0.400) | 11 (0.450) | 9/242 | NT | 49.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 13 (0.530) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 11 (0.400) | 9 (0.370) | 7/242 | NT | 44.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 13 (0.530) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1413126 = | 21 (0.760) | 6 (0.230) | 3/262 | NT | 17.6% | coding (199/489 nt) | sieB | Rac prophage; phage superinfection exclusion protein |
| ? | CP009273 | 1413206 = | 36 (1.360) | coding (279/489 nt) | sieB | Rac prophage; phage superinfection exclusion protein | |||||
| * | ? | CP009273 | = 1559498 | 15 (0.540) | 4 (0.150) | 4/260 | NT | 20.9% | coding (493/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| ? | CP009273 | = 1559747 | 16 (0.610) | coding (244/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator | |||||
| * | ? | CP009273 | = 2164908 | NA (NA) | 12 (0.440) | 11/272 | NT | 28.7% | intergenic (+29/+2) | insF1/gatR | IS3 transposase B/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| ? | CP009273 | 4283864 = | 30 (1.090) | coding (394/597 nt) | nrfG | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG | |||||
| * | ? | CP009273 | 2684986 = | 20 (0.720) | 5 (0.190) | 4/266 | NT | 20.2% | intergenic (‑287/+29) | glmY/purL | sRNA activator of glmS mRNA, glmZ processing antagonist/phosphoribosylformyl‑glycineamide synthetase |
| ? | CP009273 | 2685123 = | 20 (0.750) | coding (3780/3888 nt) | purL | phosphoribosylformyl‑glycineamide synthetase | |||||
| * | ? | CP009273 | = 2934061 | 23 (0.830) | 6 (0.230) | 6/260 | NT | 21.9% | coding (542/1101 nt) | rlmM | 23S rRNA C2498 2'‑O‑ribose methyltransferase, SAM‑dependent |
| ? | CP009273 | = 2934240 | 21 (0.800) | coding (363/1101 nt) | rlmM | 23S rRNA C2498 2'‑O‑ribose methyltransferase, SAM‑dependent | |||||
| * | ? | CP009273 | 3257426 = | 40 (1.450) | 4 (0.160) | 4/252 | NT | 12.0% | coding (951/1332 nt) | tdcC | L‑threonine/L‑serine transporter |
| ? | CP009273 | 3257509 = | 22 (0.870) | coding (868/1332 nt) | tdcC | L‑threonine/L‑serine transporter | |||||
| * | ? | CP009273 | 3295917 = | 34 (1.230) | 4 (0.150) | 3/262 | NT | 8.6% | coding (70/879 nt) | yhbV | U32 peptidase family protein |
| ? | CP009273 | 3296701 = | 53 (2.010) | coding (854/879 nt) | yhbV | U32 peptidase family protein | |||||
| * | ? | CP009273 | = 3921394 | 24 (0.870) | 4 (0.150) | 4/260 | NT | 16.1% | coding (880/993 nt) | asnA | asparagine synthetase A |
| ? | CP009273 | = 3921515 | 19 (0.730) | coding (1449/1452 nt) | viaA | stimulator of RavA ATPase activity; von Willebrand factor domain protein | |||||
| * | ? | CP009273 | = 4334267 | 43 (1.560) | 4 (0.160) | 4/254 | NT | 8.4% | coding (1082/1422 nt) | melB | melibiose:sodium symporter |
| ? | CP009273 | = 4334413 | 47 (1.840) | coding (1228/1422 nt) | melB | melibiose:sodium symporter | |||||
| * | ? | CP009273 | 4440863 = | 47 (1.700) | 4 (0.150) | 3/262 | NT | 9.5% | intergenic (+128/‑12) | ytfQ/ytfR | galactofuranose binding proteint: periplasmic‑binding component of ABC superfamily/putative ABC superfamily sugar transporter ATP‑binding subunit |
| ? | CP009273 | 4440937 = | 31 (1.170) | coding (63/1503 nt) | ytfR | putative ABC superfamily sugar transporter ATP‑binding subunit | |||||
| * | ? | CP009273 | 4514953 = | 63 (2.280) | 4 (0.150) | 4/266 | NT | 6.4% | coding (668/789 nt) | yjhI | putative DNA‑binding transcriptional regulator |
| ? | CP009273 | 4515239 = | 55 (2.050) | coding (382/789 nt) | yjhI | putative DNA‑binding transcriptional regulator | |||||
| * | ? | CP009273 | = 4572049 | 52 (1.880) | 4 (0.150) | 3/260 | NT | 7.9% | coding (817/1590 nt) | hsdM | DNA methyltransferase M |
| ? | CP009273 | = 4572174 | 44 (1.680) | coding (692/1590 nt) | hsdM | DNA methyltransferase M | |||||
| * | ? | CP009273 | = 4625452 | 40 (1.450) | 7 (0.260) | 4/264 | NT | 16.4% | coding (115/474 nt) | creA | putative periplasmic protein |
| ? | CP009273 | = 4625504 | 33 (1.240) | coding (167/474 nt) | creA | putative periplasmic protein | |||||