breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | |||||
---|---|---|---|---|---|
evidence | position | mutation | annotation | gene | description |
RA | 49,765 | C→T | intergenic (+134/‑58) | kefC → / → folA | glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase |
RA | 49,884 | C→A | P21Q (CCG→CAG) | folA → | type 3 dihydrofolate reductase |
MC JC | 1,613,631 | Δ3 bp | coding (255‑257/435 nt) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
RA | 2,236,503 | G→A | T210M (ACG→ATG) | folE ← | GTP cyclohydrolase I FolE |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
RA | 3,632,461 | T→G | L487R (CTT→CGT) | pitA → | inorganic phosphate transporter PitA |
RA | 3,754,231 | G→T | R127S (CGC→AGC) | selA ← | L‑seryl‑tRNA(Sec) selenium transferase |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 255922 | 255967 | 46 | 3 [1] | [1] 2 | phoE/proB | phosphoporin PhoE/glutamate 5‑kinase |
* | * | ÷ | NZ_CP009273 | 356981 | 357578 | 598 | 2 [0] | [1] 2 | [lacA] | [lacA] |
* | * | ÷ | NZ_CP009273 | 380412 | 380420 | 9 | 2 [0] | [1] 3 | BW25113_RS01880/tauA | PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein |
* | * | ÷ | NZ_CP009273 | 632184 | 632238 | 55 | 2 [1] | [1] 2 | ybdO | LysR family transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 703451 | 703540 | 90 | 5 [1] | [1] 2 | glnS/chiP | glutamine‑‑tRNA ligase/chitoporin |
* | * | ÷ | NZ_CP009273 | 729236 | 729266 | 31 | 2 [1] | [0] 4 | BW25113_RS03630 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 982718 | 982728 | 11 | 2 [0] | [1] 2 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 1051176 | 1051188 | 13 | 2 [0] | [0] 2 | torS | TMAO reductase system sensor histidine kinase/response regulator TorS |
* | * | ÷ | NZ_CP009273 | 1158327 | 1158352 | 26 | 2 [1] | [1] 3 | lpoB | penicillin‑binding protein activator LpoB |
* | * | ÷ | NZ_CP009273 | 1207066 | 1207129 | 64 | 2 [1] | [1] 3 | BW25113_RS23640/iraM | isocitrate/isopropylmalate family dehydrogenase/anti‑adapter protein IraM |
* | * | ÷ | NZ_CP009273 | 1229286 | 1229315 | 30 | 2 [1] | [0] 2 | nhaB | Na(+)/H(+) antiporter NhaB |
* | * | ÷ | NZ_CP009273 | 1281532 | 1281551 | 20 | 2 [0] | [1] 2 | narI | respiratory nitrate reductase subunit gamma |
* | * | ÷ | NZ_CP009273 | 1305425 | 1305430 | 6 | 2 [0] | [0] 4 | tonB | TonB system transport protein TonB |
* | * | ÷ | NZ_CP009273 | 1427977–1428258 | 1428279 | 22–303 | 3 [1] | [1] 2 | [ydfK] | [ydfK] |
* | * | ÷ | NZ_CP009273 | 1524310 | 1524427 | 118 | 2 [0] | [1] 4 | [BW25113_RS26145] | [BW25113_RS26145] |
* | * | ÷ | NZ_CP009273 | 1594169 | 1594169 | 1 | 4 [0] | [0] 5 | lsrK | autoinducer‑2 kinase |
* | * | ÷ | NZ_CP009273 | 1617039 | 1617044 | 6 | 3 [0] | [1] 2 | mgtT | protein MgtT |
* | * | ÷ | NZ_CP009273 | 1646931 | 1646952 | 22 | 2 [1] | [1] 2 | BW25113_RS25635 | tyrosine‑type recombinase/integrase |
* | * | ÷ | NZ_CP009273 | 1748938 | 1748976 | 39 | 2 [1] | [1] 2 | ydhY/fumD | ferredoxin‑like protein/fumarate hydratase FumD |
* | * | ÷ | NZ_CP009273 | 1757738 | 1757743 | 6 | 2 [1] | [1] 2 | sufB | Fe‑S cluster assembly protein SufB |
* | * | ÷ | NZ_CP009273 | 1864569 | 1864630 | 62 | 2 [1] | [1] 2 | yeaH/cdgI | YeaH/YhbH family protein/GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1940855 | 1940925 | 71 | 2 [1] | [1] 2 | yebB | YebB family permuted papain‑like enzyme |
* | * | ÷ | NZ_CP009273 | 1946078 | 1946121 | 44 | 3 [1] | [1] 2 | yecE | DUF72 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2024381 | 2024404 | 24 | 2 [1] | [1] 4 | dcm | DNA‑cytosine methyltransferase |
* | * | ÷ | NZ_CP009273 | 2027032 | 2027124 | 93 | 2 [1] | [1] 2 | drpB/ompC | cell division protein DrpB/porin OmpC |
* | * | ÷ | NZ_CP009273 | 2050102 | 2050191 | 90 | 3 [1] | [1] 2 | amn/yeeN | AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 2051100 | 2051153 | 54 | 2 [0] | [0] 4 | yeeN/BW25113_RS10360 | YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn |
* | * | ÷ | NZ_CP009273 | 2097466 | 2097517 | 52 | 2 [1] | [1] 3 | wbbK | glycosyltransferase family 1 protein |
* | * | ÷ | NZ_CP009273 | 2100158 | 2100210 | 53 | 3 [1] | [1] 2 | wzy | O16 family O‑antigen polymerase |
* | * | ÷ | NZ_CP009273 | 2101611 | 2101661 | 51 | 2 [1] | [1] 2 | glf | UDP‑galactopyranose mutase |
* | * | ÷ | NZ_CP009273 | 2170672 | 2170694 | 23 | 2 [0] | [1] 3 | [gatY] | [gatY] |
* | * | ÷ | NZ_CP009273 | 2185806 | 2185840 | 35 | 2 [0] | [1] 2 | yehD/yehE | fimbrial protein/YehE family protein |
* | * | ÷ | NZ_CP009273 | 2357920 | 2357965 | 46 | 2 [1] | [1] 2 | yfaZ/nudI | YfaZ family protein/nucleoside triphosphatase NudI |
* | * | ÷ | NZ_CP009273 | 2463684 | 2463768 | 85 | 5 [1] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2463844 | 2463868 | 25 | 2 [0] | [1] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2768270 | 2768299 | 30 | 2 [1] | [1] 2 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2897122 | 2897184 | 63 | 2 [1] | [1] 2 | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
* | * | ÷ | NZ_CP009273 | 2988549 | 2988597 | 49 | 2 [1] | [1] 2 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3178654 | 3178735 | 82 | 2 [1] | [1] 2 | ubiK/ygiL | ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein |
* | * | ÷ | NZ_CP009273 | 3463354 | 3463400 | 47 | 2 [1] | [1] 2 | chiA/tuf | bifunctional chitinase/lysozyme/elongation factor Tu |
* | * | ÷ | NZ_CP009273 | 3576003 | 3576006 | 4 | 4 [0] | [0] 2 | hcp | Hcp1 family type VI secretion system effector |
* | * | ÷ | NZ_CP009273 | 3792637 | 3792686 | 50 | 2 [1] | [1] 2 | [waaU] | [waaU] |
* | * | ÷ | NZ_CP009273 | 4258769 | 4258825 | 57 | 2 [1] | [1] 2 | BW25113_RS26020 | hypothetical protein |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 269666 = | NA (NA) | 19 (0.930) | 8/166 | 0.8 | 100% | intergenic (+2/+146) | ykfC/BW25113_RS01325 | reverse transcriptase domain‑containing protein/IS5‑like element IS5 family transposase |
? | NZ_CP009273 | = 481436 | 0 (0.000) | coding (220/648 nt) | acrR | multidrug efflux transporter transcriptional repressor AcrR | |||||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 49 (2.390) | 28/166 | 0.0 | NA | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
? | NZ_CP009273 | = 360286 | NA (NA) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
* | ? | NZ_CP009273 | 481433 = | 0 (0.000) | 26 (1.270) | 19/166 | 0.1 | 100% | coding (217/648 nt) | acrR | multidrug efflux transporter transcriptional repressor AcrR |
? | NZ_CP009273 | = 571241 | NA (NA) | coding (1041/1068 nt) | BW25113_RS02855 | porin | |||||
* | ? | NZ_CP009273 | 1203246 = | 2 (0.100) | 11 (0.670) | 10/134 | 0.4 | 85.9% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 2 (0.120) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1203261 | 2 (0.100) | 5 (0.300) | 3/134 | 1.4 | 73.5% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | = 1205058 | 2 (0.120) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 12 (0.590) | 8/164 | 0.7 | 100% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1972747 = | 0 (0.000) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 24 (1.170) | 18/166 | 0.2 | 100% | intergenic (‑297/‑483) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
? | NZ_CP009273 | = 2283592 | NA (NA) | intergenic (‑68/‑387) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP | |||||
* | ? | NZ_CP009273 | 4532499 = | 3 (0.150) | 13 (0.710) | 9/148 | 0.5 | 77.2% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | 4532813 = | 5 (0.270) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |