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 | 1,613,576 | A→C | D67A (GAC→GCC) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 235120 | 235139 | 20 | 3 [0] | [1] 2 | BW25113_RS01095 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 356966 | 357567 | 602 | 2 [1] | [0] 2 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 428519 | 428539 | 21 | 2 [1] | [0] 2 | nrdR | transcriptional regulator NrdR |
* | * | ÷ | NZ_CP009273 | 472110 | 472125 | 16 | 2 [1] | [0] 2 | ffs/ybaA | signal recognition particle sRNA small type/DUF1428 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 476533 | 476576 | 44 | 2 [1] | [1] 2 | tomB/acrB | Hha toxicity modulator TomB/efflux RND transporter permease AcrB |
* | * | ÷ | NZ_CP009273 | 523342 | 523399 | 58 | 2 [1] | [1] 3 | ybbC | YbbC/YhhH family protein |
* | * | ÷ | NZ_CP009273 | 532831 | 532837 | 7 | 2 [1] | [1] 3 | glxR | 2‑hydroxy‑3‑oxopropionate reductase |
* | * | ÷ | NZ_CP009273 | 600235 | 600251 | 17 | 2 [0] | [1] 2 | nfsB | oxygen‑insensitive NAD(P)H nitroreductase |
* | * | ÷ | NZ_CP009273 | 618484 | 618488 | 5 | 2 [1] | [0] 2 | entS | enterobactin transporter EntS |
* | * | ÷ | NZ_CP009273 | 656858 | 656890 | 33 | 2 [1] | [1] 2 | ybeF/lipB | YbeF family transcriptional regulator/lipoyl(octanoyl) transferase LipB |
* | * | ÷ | NZ_CP009273 | 674899 | 674928 | 30 | 3 [1] | [1] 2 | ybeT/ybeU | tetratricopeptide repeat protein/DUF1266 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 703923 | 703931 | 9 | 2 [1] | [0] 4 | chiP | chitoporin |
* | * | ÷ | NZ_CP009273 | 716379 | 716416 | 38 | 2 [1] | [0] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 769935 | 769972 | 38 | 2 [1] | [1] 2 | ybgE | cyd operon protein YbgE |
* | * | ÷ | NZ_CP009273 | 772345 | 772355 | 11 | 2 [1] | [0] 2 | tolA | cell envelope integrity protein TolA |
* | * | ÷ | NZ_CP009273 | 860465 | 860486 | 22 | 2 [0] | [1] 3 | moeB | molybdopterin‑synthase adenylyltransferase MoeB |
* | * | ÷ | NZ_CP009273 | 864517 | 864575 | 59 | 2 [1] | [1] 2 | gsiA | glutathione ABC transporter ATP‑binding protein GsiA |
* | * | ÷ | NZ_CP009273 | 868454 | 868516 | 63 | 2 [1] | [0] 2 | pdeI | EAL domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 950178 | 950212 | 35 | 2 [0] | [1] 2 | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
* | * | ÷ | NZ_CP009273 | 993220 | 993267 | 48 | 3 [1] | [1] 2 | ssuE/elfA | NADPH‑dependent FMN reductase/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1016561 | 1016590 | 30 | 2 [1] | [1] 2 | sulA/sxy | cell division inhibitor SulA/CRP‑S regulon transcriptional coactivator Sxy |
* | * | ÷ | NZ_CP009273 | 1032517 | 1032589 | 73 | 2 [1] | [1] 2 | hyaF | hydrogenase expression/formation protein |
* | * | ÷ | NZ_CP009273 | 1032702 | 1032717 | 16 | 2 [0] | [1] 2 | hyaF | hydrogenase expression/formation protein |
* | * | ÷ | NZ_CP009273 | 1088096 | 1088106 | 11 | 2 [0] | [1] 2 | pgaA/dgcT | poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1113803 | 1113816 | 14 | 2 [0] | [1] 2 | yceI | YceI family protein |
* | * | ÷ | NZ_CP009273 | 1164353 | 1164420 | 68 | 2 [1] | [1] 2 | comR/bhsA | TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA |
* | * | ÷ | NZ_CP009273 | 1165713 | 1165750 | 38 | 2 [1] | [0] 2 | ldtC | L,D‑transpeptidase LdtC |
* | * | ÷ | NZ_CP009273 | 1205059 | 1205074 | 16 | 15 [0] | [0] 7 | BW25113_RS06005 | phage tail protein |
* | * | ÷ | NZ_CP009273 | 1211816 | 1211836 | 21 | 4 [1] | [0] 4 | [ariR] | [ariR] |
* | * | ÷ | NZ_CP009273 | 1225762 | 1225785 | 24 | 2 [1] | [1] 2 | hlyE | hemolysin HlyE |
* | * | ÷ | NZ_CP009273 | 1301408 | 1301418 | 11 | 2 [1] | [0] 2 | yciU/cls | HI1450 family dsDNA‑mimic protein/cardiolipin synthase |
* | * | ÷ | NZ_CP009273 | 1433488 | 1433498 | 11 | 2 [0] | [1] 2 | nifJ | pyruvate:ferredoxin (flavodoxin) oxidoreductase |
* | * | ÷ | NZ_CP009273 | 1445116 | 1445139 | 24 | 2 [1] | [1] 2 | tynA | primary‑amine oxidase |
* | * | ÷ | NZ_CP009273 | 1461155 | 1461163 | 9 | 2 [1] | [1] 2 | BW25113_RS07350 | autotransporter domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1476925 | 1476994 | 70 | 2 [1] | [1] 3 | azoR | FMN‑dependent NADH‑azoreductase |
* | * | ÷ | NZ_CP009273 | 1486698 | 1486707 | 10 | 3 [0] | [1] 2 | BW25113_RS26140/trg | hypothetical protein/methyl‑accepting chemotaxis protein Trg |
* | * | ÷ | NZ_CP009273 | 1524312 | 1524394 | 83 | 3 [1] | [1] 2 | BW25113_RS07645/BW25113_RS26145 | RHS repeat protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1528460 | 1528497 | 38 | 2 [1] | [0] 2 | nhoA | N‑hydroxyarylamine O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 1595183 | 1595192 | 10 | 2 [1] | [0] 2 | lsrR | transcriptional regulator LsrR |
* | * | ÷ | NZ_CP009273 | 1622885 | 1622899 | 15 | 2 [1] | [1] 2 | ydfH | DNA‑binding transcriptional regulator rspR |
* | * | ÷ | NZ_CP009273 | 1658114 | 1658123 | 10 | 2 [1] | [0] 2 | ynfH | dimethyl sulfoxide reductase anchor subunit |
* | * | ÷ | NZ_CP009273 | 1663836 | 1663920 | 85 | 2 [1] | [1] 2 | [ynfL] | [ynfL] |
* | * | ÷ | NZ_CP009273 | 1725387 | 1725411 | 25 | 2 [0] | [1] 2 | lhr | ATP‑dependent helicase |
* | * | ÷ | NZ_CP009273 | 1725650 | 1725714 | 65 | 2 [1] | [1] 2 | lhr | ATP‑dependent helicase |
* | * | ÷ | NZ_CP009273 | 1800462 | 1800492 | 31 | 3 [0] | [1] 2 | ydiY/pfkB | YdiY family protein/6‑phosphofructokinase II |
* | * | ÷ | NZ_CP009273 | 1839514 | 1839538 | 25 | 2 [1] | [1] 2 | topB | DNA topoisomerase III |
* | * | ÷ | NZ_CP009273 | 1841779 | 1841869 | 91 | 2 [1] | [1] 2 | selD | selenide, water dikinase SelD |
* | * | ÷ | NZ_CP009273 | 1972752 | 1972760 | 9 | 16 [0] | [1] 2 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
* | * | ÷ | NZ_CP009273 | 1982093 | 1982099 | 7 | 3 [0] | [1] 2 | yecR/ftnA | YecR‑like lipofamily protein/non‑heme ferritin |
* | * | ÷ | NZ_CP009273 | 1994548 | 1994579 | 32 | 3 [1] | [1] 2 | [fliA] | [fliA] |
* | * | ÷ | NZ_CP009273 | 2035752 | 2035796 | 45 | 3 [1] | [1] 2 | zinT/yodB | metal‑binding protein ZinT/cytochrome b |
* | * | ÷ | NZ_CP009273 | 2078236 | 2078246 | 11 | 3 [1] | [1] 2 | yeeE | thiosulfate utilization transporter TsuA/YeeE |
* | * | ÷ | NZ_CP009273 | 2152844 | 2152937 | 94 | 2 [1] | [0] 2 | mdtC | multidrug efflux RND transporter permease subunit MdtC |
* | * | ÷ | NZ_CP009273 | 2243113 | 2243159 | 47 | 2 [1] | [1] 2 | yeiE/yeiH | DNA‑binding transcriptional regulator YeiE/YeiH family protein |
* | * | ÷ | NZ_CP009273 | 2257456 | 2257481 | 26 | 3 [1] | [0] 3 | setB | sugar efflux transporter SetB |
* | * | ÷ | NZ_CP009273 | 2337795 | 2337840 | 46 | 2 [1] | [0] 2 | yfaL/nrdA | AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 2348038 | 2348066 | 29 | 2 [1] | [1] 3 | glpB | glycerol‑3‑phosphate dehydrogenase subunit GlpB |
* | * | ÷ | NZ_CP009273 | 2348322 | 2348330 | 9 | 2 [0] | [0] 2 | glpB | glycerol‑3‑phosphate dehydrogenase subunit GlpB |
* | * | ÷ | NZ_CP009273 | 2371940 | 2371965 | 26 | 2 [1] | [1] 2 | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase |
* | * | ÷ | NZ_CP009273 | 2376886 | 2376938 | 53 | 2 [1] | [1] 2 | elaD | deubiquitinase ElaD |
* | * | ÷ | NZ_CP009273 | 2553589 | 2553610 | 22 | 4 [1] | [1] 2 | intZ/BW25113_RS12740 | integrase arm‑type DNA‑binding domain‑containing protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2559185 | 2559190 | 6 | 2 [1] | [0] 2 | eutA | ethanolamine ammonia‑lyase reactivating factor EutA |
* | * | ÷ | NZ_CP009273 | 2563818 | 2563838 | 21 | 2 [0] | [1] 2 | eutE | aldehyde dehydrogenase EutE |
* | * | ÷ | NZ_CP009273 | 2590640 | 2590665 | 26 | 2 [0] | [1] 2 | purC | phosphoribosylaminoimidazolesuccinocarboxamide synthase |
* | * | ÷ | NZ_CP009273 | 2608191 | 2608219 | 29 | 3 [1] | [1] 3 | yfgO | AI‑2E family transporter |
* | * | ÷ | NZ_CP009273 | 2687778 | 2687812 | 35 | 2 [1] | [1] 2 | purL | phosphoribosylformylglycinamidine synthase |
* | * | ÷ | NZ_CP009273 | 2767746 | 2767818 | 73 | 2 [1] | [1] 2 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2767936 | 2767962 | 27 | 2 [1] | [1] 3 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2828071 | 2828115 | 45 | 2 [1] | [1] 2 | norW | NADH:flavorubredoxin reductase NorW |
* | * | ÷ | NZ_CP009273 | 2897187 | 2897208 | 22 | 2 [1] | [1] 2 | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
* | * | ÷ | NZ_CP009273 | 2899870 | 2899907 | 38 | 3 [0] | [1] 2 | ygcG | YgcG family protein |
* | * | ÷ | NZ_CP009273 | 3129928 | 3129960 | 33 | 2 [0] | [1] 2 | pitB/gss | inorganic phosphate transporter PitB/bifunctional glutathionylspermidine amidase/synthase |
* | * | ÷ | NZ_CP009273 | 3227061 | 3227067 | 7 | 2 [0] | [1] 2 | fadH/higA | NADPH‑dependent 2,4‑dienoyl‑CoA reductase/type II toxin‑antitoxin system antitoxin HigA |
* | * | ÷ | NZ_CP009273 | 3348744 | 3348748 | 5 | 4 [0] | [1] 3 | gltB | glutamate synthase large subunit |
* | * | ÷ | NZ_CP009273 | 3354270 | 3354288 | 19 | 2 [1] | [1] 2 | gltD/gltF | glutamate synthase subunit GltD/DUF1120 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 3533012 | 3533018 | 7 | 3 [1] | [0] 2 | yhgF | Tex family protein |
* | * | ÷ | NZ_CP009273 | 3629247 | 3631082 | 1836 | 22 [0] | [0] 2 | [yhiM]–[pitA] | [yhiM],yhiN,[pitA] |
* | * | ÷ | NZ_CP009273 | 3631131 | 3631604 | 474 | 2 [0] | [0] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3631688 | 3633223 | 1536 | 2 [0] | [1] 2 | [pitA]–uspB | [pitA],uspB |
* | * | ÷ | NZ_CP009273 | 3633261 | 3634583 | 1323 | 2 [1] | [1] 2 | uspA–[dtpB] | uspA,BW25113_RS26225,BW25113_RS26230,[dtpB] |
* | * | ÷ | NZ_CP009273 | 3634600 | 3634697 | 98 | 2 [1] | [0] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3634777 | 3635118 | 342 | 2 [0] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635206 | 3635298 | 93 | 2 [1] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635389 | 3636121 | 733 | 2 [1] | [1] 2 | [dtpB]–[rsmJ] | [dtpB],[rsmJ] |
* | * | ÷ | NZ_CP009273 | 3636202 | 3637124 | 923 | 2 [1] | [1] 2 | [rsmJ]–[prlC] | [rsmJ],[prlC] |
* | * | ÷ | NZ_CP009273 | 3637215 | 3637414 | 200 | 2 [1] | [0] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3637475 | 3637634 | 160 | 2 [0] | [1] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3637645 | 3637833 | 189 | 2 [1] | [1] 3 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3637897 | 3640799 | 2903 | 3 [1] | [1] 2 | [prlC]–[gorA] | [prlC],rlmJ,[gorA] |
* | * | ÷ | NZ_CP009273 | 3640953 | 3641700 | 748 | 2 [1] | [0] 2 | [gorA]–dinQ | [gorA],dinQ |
* | * | ÷ | NZ_CP009273 | 3641789 | 3643123 | 1335 | 2 [0] | [1] 2 | arsR–[arsB] | arsR,[arsB] |
* | * | ÷ | NZ_CP009273 | 3643272 | 3644188 | 917 | 2 [1] | [1] 2 | [arsB]–arsC | [arsB],arsC |
* | * | ÷ | NZ_CP009273 | 3644251 | 3644409 | 159 | 2 [1] | [0] 2 | arsC/BW25113_RS18155 | glutaredoxin‑dependent arsenate reductase/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3644466 | 3644681 | 216 | 2 [0] | [1] 2 | [BW25113_RS18155] | [BW25113_RS18155] |
* | * | ÷ | NZ_CP009273 | 3644721 | 3644830 | 110 | 2 [1] | [1] 2 | BW25113_RS18155 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3644886 | 3646532–3645398 | 513–1647 | 2 [1] | [1] 2 | [BW25113_RS18155]–BW25113_RS18160 | [BW25113_RS18155],BW25113_RS18160 |
* | * | ÷ | NZ_CP009273 | 3745310 | 3745325 | 16 | 4 [1] | [0] 2 | yiaT/yiaU | MipA/OmpV family protein/LysR family transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 3787053 | 3787104 | 52 | 2 [1] | [0] 3 | yibB/rfaD | protein YibB/ADP‑glyceromanno‑heptose 6‑epimerase |
* | * | ÷ | NZ_CP009273 | 4205321 | 4205329 | 9 | 2 [0] | [1] 2 | metA/aceB | homoserine O‑succinyltransferase/malate synthase A |
* | * | ÷ | NZ_CP009273 | 4532462 | 4532537 | 76 | 2 [0] | [1] 3 | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 38 (2.520) | 20/166 | 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 | 1203246 = | 0 (0.000) | 5 (0.410) | 5/134 | 0.7 | 100% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 0 (0.000) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1203261 | 0 (0.000) | 14 (1.150) | 14/134 | 0.1 | 100% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | = 1205058 | 0 (0.000) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391495 | NA (NA) | 6 (0.400) | 6/166 | 0.8 | 100% | intergenic (+146/‑127) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1903069 = | 0 (0.000) | intergenic (‑46/‑113) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein | |||||
* | ? | NZ_CP009273 | = 1903072 | 0 (0.000) | 11 (0.730) | 11/166 | 0.3 | 100% | intergenic (‑49/‑110) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein |
? | NZ_CP009273 | = 2096424 | NA (NA) | intergenic (‑68/+3) | BW25113_RS10605/wbbL | IS5‑like element IS5 family transposase/N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 16 (1.060) | 14/166 | 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 | 2282398 = | NA (NA) | 23 (1.530) | 13/166 | 0.2 | 92.0% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
? | NZ_CP009273 | 3512437 = | 2 (0.130) | intergenic (‑14/+387) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
* | ? | NZ_CP009273 | = 2283591 | NA (NA) | 27 (1.810) | 18/164 | 0.1 | 93.2% | intergenic (‑67/‑388) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
? | NZ_CP009273 | = 3512441 | 2 (0.130) | intergenic (‑18/+383) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
* | ? | NZ_CP009273 | = 3629246 | 0 (0.000) | 21 (1.390) | 8/166 | 0.5 | 100% | coding (1046/1053 nt) | yhiM | DUF2776 domain‑containing protein |
? | NZ_CP009273 | 3645396 = | NA (NA) | pseudogene (746/747 nt) | BW25113_RS18155 | hypothetical protein |