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 | 49,791 | G→A | intergenic (+160/‑32) | kefC → / → folA | glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase |
RA | 1,902,968 | Δ1 bp | coding (56/144 nt) | mgrB ← | PhoP/PhoQ regulator MgrB |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
RA | 3,754,231 | G→T | R127S (CGC→AGC) | selA ← | L‑seryl‑tRNA(Sec) selenium transferase |
JC | 4,267,801 | +CCG | coding (405/465 nt) | soxR → | redox‑sensitive transcriptional activator SoxR |
RA | 4,458,295 | T→G | I285S (ATC→AGC) | mgtA → | magnesium‑translocating P‑type ATPase |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356968 | 357570 | 603 | 2 [1] | [1] 2 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 578972 | 579033 | 62 | 2 [1] | [1] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 647607 | 647617 | 11 | 2 [1] | [0] 2 | citC/dpiB | [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB |
* | * | ÷ | NZ_CP009273 | 716379 | 716452 | 74 | 2 [1] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 987880 | 987895 | 16 | 3 [0] | [1] 3 | pepN | aminopeptidase N |
* | * | ÷ | NZ_CP009273 | 993134 | 993278 | 145 | 2 [1] | [1] 2 | ssuE/elfA | NADPH‑dependent FMN reductase/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1059485 | 1059495 | 11 | 2 [1] | [1] 4 | [yccE] | [yccE] |
* | * | ÷ | NZ_CP009273 | 1192717 | 1192796 | 80 | 2 [1] | [1] 2 | ymfD | class I SAM‑dependent methyltransferase |
* | * | ÷ | NZ_CP009273 | 1206620 | 1206671 | 52 | 4 [1] | [0] 2 | [mcrA] | [mcrA] |
* | * | ÷ | NZ_CP009273 | 1207528 | 1207531 | 4 | 4 [0] | [0] 2 | iraM/BW25113_RS25985 | anti‑adapter protein IraM/protein YmgK |
* | * | ÷ | NZ_CP009273 | 1380783 | 1380804 | 22 | 5 [0] | [1] 2 | ycjF | YcjF family protein |
* | * | ÷ | NZ_CP009273 | 1380903 | 1380939 | 37 | 2 [1] | [1] 4 | ycjF/tyrR | YcjF family protein/transcriptional regulator TyrR |
* | * | ÷ | NZ_CP009273 | 1389956 | 1390000 | 45 | 2 [1] | [1] 2 | ynaI | low conductance mechanosensitive channel YnaI |
* | * | ÷ | NZ_CP009273 | 1459390 | 1459516 | 127 | 2 [1] | [0] 2 | BW25113_RS25580 | BW25113_RS25580 |
* | * | ÷ | NZ_CP009273 | 1485766 | 1485783 | 18 | 2 [0] | [0] 2 | cybB/BW25113_RS07445 | cytochrome b561/periplasmic protein |
* | * | ÷ | NZ_CP009273 | 1521283 | 1521366 | 84 | 2 [0] | [1] 2 | yncH | YncH family protein |
* | * | ÷ | NZ_CP009273 | 1521556 | 1521575 | 20 | 2 [1] | [0] 3 | yncH/BW25113_RS07645 | YncH family protein/RHS repeat protein |
* | * | ÷ | NZ_CP009273 | 1581017 | 1581029 | 13 | 2 [0] | [1] 3 | ydeP/ydeQ | acid resistance putative oxidoreductase YdeP/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1618523 | 1618540 | 18 | 5 [0] | [1] 3 | ydeI | YdeI family stress tolerance OB fold protein |
* | * | ÷ | NZ_CP009273 | 1631426 | 1631462 | 37 | 2 [1] | [0] 2 | ydfO | DUF1398 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1632902 | 1632934 | 33 | 2 [0] | [0] 4 | [cspI] | [cspI] |
* | * | ÷ | NZ_CP009273 | 1635220 | 1635285 | 66 | 8 [1] | [1] 5 | [ynfU] | [ynfU] |
* | * | ÷ | NZ_CP009273 | 1750082 | 1750119 | 38 | 2 [1] | [0] 2 | pykF | pyruvate kinase PykF |
* | * | ÷ | NZ_CP009273 | 1864867 | 1864870 | 4 | 2 [0] | [0] 3 | cdgI | GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1896099 | 1896155 | 57 | 2 [1] | [1] 3 | yoaE/manX | CNNM family cation transport protein YoaE/PTS mannose transporter subunit IIAB |
* | * | ÷ | NZ_CP009273 | 1912822 | 1912830 | 9 | 2 [0] | [1] 3 | yebT | lipid‑binding membrane homeostasis protein YebT |
* | * | ÷ | NZ_CP009273 | 1980209 | 1980254 | 46 | 2 [1] | [0] 2 | araF/ftnB | arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein |
* | * | ÷ | NZ_CP009273 | 2004882 | 2004902 | 21 | 2 [1] | [0] 3 | BW25113_RS10120 | DUF5503 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2008597 | 2008602 | 6 | 2 [0] | [1] 3 | fliG | flagellar motor switch protein FliG |
* | * | ÷ | NZ_CP009273 | 2027317 | 2027372 | 56 | 2 [0] | [1] 2 | drpB/ompC | cell division protein DrpB/porin OmpC |
* | * | ÷ | NZ_CP009273 | 2050211 | 2050277 | 67 | 2 [1] | [1] 3 | amn/yeeN | AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 2246110 | 2246126 | 17 | 2 [1] | [1] 4 | yeiI | sugar kinase |
* | * | ÷ | NZ_CP009273 | 2370758 | 2370816 | 59 | 2 [1] | [1] 2 | menH | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
* | * | ÷ | NZ_CP009273 | 2462809 | 2462859 | 51 | 2 [0] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2462907 | 2462937 | 31 | 2 [0] | [1] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2463057 | 2463069 | 13 | 2 [0] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2622497 | 2622540 | 44 | 2 [0] | [1] 3 | BW25113_RS25940 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2622952 | 2623015 | 64 | 3 [1] | [1] 2 | yfgG/yfgH | YfgG family protein/glycine zipper 2TM domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2768272 | 2768289 | 18 | 2 [1] | [1] 3 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2776935 | 2776949 | 15 | 3 [1] | [1] 3 | BW25113_RS24210/BW25113_RS25705 | recombinase family protein/DUF5507 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2897127 | 2897257 | 131 | 2 [1] | [1] 2 | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
* | * | ÷ | NZ_CP009273 | 2988539 | 2988660 | 122 | 3 [1] | [1] 3 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3463343 | 3463398 | 56 | 2 [1] | [1] 2 | chiA/tuf | bifunctional chitinase/lysozyme/elongation factor Tu |
* | * | ÷ | NZ_CP009273 | 3745315 | 3745334 | 20 | 2 [0] | [1] 2 | yiaT/yiaU | MipA/OmpV family protein/LysR family transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 3798414 | 3798447 | 34 | 2 [0] | [0] 2 | rfaS | LPS core biosynthesis protein RfaS |
* | * | ÷ | NZ_CP009273 | 4080238 | 4080329 | 92 | 2 [1] | [1] 2 | fdhD/yiiG | formate dehydrogenase accessory sulfurtransferase FdhD/YiiG family protein |
* | * | ÷ | NZ_CP009273 | 4531411 | 4531421 | 11 | 2 [1] | [0] 2 | fimB/fimE | type 1 fimbria switch DNA invertase FimB/type 1 fimbria switch DNA invertase FimE |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 23 (1.390) | 13/166 | 0.3 | 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 | 1203246 = | 10 (0.600) | 12 (0.900) | 12/134 | 0.2 | 63.0% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 6 (0.450) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1203261 | 10 (0.600) | 8 (0.600) | 8/134 | 0.4 | 53.2% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | = 1205058 | 6 (0.450) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 8 (0.490) | 6/164 | 0.9 | 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 | 1 (0.060) | 28 (1.690) | 19/166 | 0.1 | 96.5% | 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 | 2282398 = | NA (NA) | 17 (1.020) | 9/166 | 0.5 | 100% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
? | NZ_CP009273 | 3512437 = | 0 (0.000) | intergenic (‑14/+387) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
* | ? | NZ_CP009273 | = 2283591 | NA (NA) | 25 (1.530) | 17/164 | 0.1 | 86.4% | intergenic (‑67/‑388) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
? | NZ_CP009273 | = 3512441 | 4 (0.240) | intergenic (‑18/+383) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ |