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 | 49,912 | G→T | W30C (TGG→TGT) | folA → | type 3 dihydrofolate reductase |
RA | 214,743 | A→C | Y174D (TAC→GAC) | proS ← | proline‑‑tRNA ligase |
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 |
RA | 4,267,454 | C→T | R20C (CGC→TGC) | soxR → | redox‑sensitive transcriptional activator SoxR |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356981 | 357569 | 589 | 3 [0] | [1] 3 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 396670 | 396700 | 31 | 2 [1] | [1] 2 | BW25113_RS25915/iraP | hypothetical protein/anti‑adapter protein IraP |
* | * | ÷ | NZ_CP009273 | 578967 | 578997 | 31 | 2 [1] | [1] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 716403 | 716491 | 89 | 2 [1] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 724408 | 724461 | 54 | 2 [1] | [1] 2 | kdpF/ybfA | K(+)‑transporting ATPase subunit F/YbfA family protein |
* | * | ÷ | NZ_CP009273 | 837037 | 837050 | 14 | 2 [1] | [1] 3 | fiu/mcbA | catecholate siderophore receptor Fiu/DUF1471 family periplasmic protein McbA |
* | * | ÷ | NZ_CP009273 | 950171 | 950219 | 49 | 2 [1] | [1] 2 | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
* | * | ÷ | NZ_CP009273 | 1193193 | 1193262 | 70 | 2 [1] | [1] 2 | BW25113_RS05920 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1205776 | 1205806 | 31 | 2 [1] | [1] 3 | [mcrA] | [mcrA] |
* | * | ÷ | NZ_CP009273 | 1212091 | 1212113 | 23 | 2 [0] | [1] 2 | [ariR] | [ariR] |
* | * | ÷ | NZ_CP009273 | 1431318 | 1431373 | 56 | 2 [1] | [1] 3 | ompN/nifJ | porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase |
* | * | ÷ | NZ_CP009273 | 1524310 | 1524340 | 31 | 2 [1] | [1] 3 | BW25113_RS07645/BW25113_RS26145 | RHS repeat protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1540318 | 1540420 | 103 | 2 [1] | [1] 2 | yddL/yddG | porin/aromatic amino acid efflux DMT transporter YddG |
* | * | ÷ | NZ_CP009273 | 1567137 | 1567147 | 11 | 2 [0] | [1] 3 | pqqL | insulinase family protein |
* | * | ÷ | NZ_CP009273 | 1783818 | 1783881 | 64 | 3 [1] | [0] 4 | [hemP] | [hemP] |
* | * | ÷ | NZ_CP009273 | 1899534 | 1899572 | 39 | 2 [1] | [1] 2 | yobD/mntP | DUF986 family protein/manganese efflux pump MntP |
* | * | ÷ | NZ_CP009273 | 1972752 | 1972775 | 24 | 30 [0] | [1] 2 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
* | * | ÷ | NZ_CP009273 | 2097490 | 2097570 | 81 | 2 [1] | [0] 2 | wbbK | glycosyltransferase family 1 protein |
* | * | ÷ | NZ_CP009273 | 2100145 | 2100208 | 64 | 2 [1] | [1] 2 | wzy | O16 family O‑antigen polymerase |
* | * | ÷ | NZ_CP009273 | 2449323 | 2449367 | 45 | 3 [1] | [1] 2 | yfcV/sixA | fimbrial protein/phosphohistidine phosphatase SixA |
* | * | ÷ | NZ_CP009273 | 2462860 | 2462908 | 49 | 2 [1] | [1] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2779386 | 2779392 | 7 | 2 [1] | [0] 2 | BW25113_RS13825/BW25113_RS26005 | tRNA‑Ile/alpha‑amylase family glycosyl hydrolase |
* | * | ÷ | NZ_CP009273 | 2779430 | 2779464 | 35 | 2 [0] | [1] 2 | BW25113_RS13825/BW25113_RS26005 | tRNA‑Ile/alpha‑amylase family glycosyl hydrolase |
* | * | ÷ | NZ_CP009273 | 2819106 | 2819145 | 40 | 3 [1] | [1] 7 | mltB/srlA | lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC |
* | * | ÷ | NZ_CP009273 | 3044356 | 3044362 | 7 | 2 [1] | [0] 5 | BW25113_RS25745 | protein YqfI |
* | * | ÷ | NZ_CP009273 | 3178740 | 3178750 | 11 | 2 [0] | [0] 2 | ubiK/ygiL | ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein |
* | * | ÷ | NZ_CP009273 | 3354473 | 3354480 | 8 | 2 [0] | [1] 3 | gltD/gltF | glutamate synthase subunit GltD/DUF1120 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 3406917 | 3406966 | 50 | 2 [0] | [1] 2 | acrS/acrE | multidrug efflux transporter transcriptional repressor AcrS/multidrug efflux RND transporter periplasmic adaptor subunit AcrE |
* | * | ÷ | NZ_CP009273 | 3763017 | 3763127 | 111 | 2 [1] | [1] 2 | BW25113_RS26240 | Imm57 family immunity protein |
* | * | ÷ | NZ_CP009273 | 3787031 | 3787095 | 65 | 2 [1] | [1] 2 | [yibB] | [yibB] |
* | * | ÷ | NZ_CP009273 | 3798187 | 3798216 | 30 | 2 [1] | [0] 2 | rfaS | LPS core biosynthesis protein RfaS |
* | * | ÷ | NZ_CP009273 | 3798345 | 3798474 | 130 | 2 [1] | [1] 2 | rfaS | LPS core biosynthesis protein RfaS |
* | * | ÷ | NZ_CP009273 | 3979613 | 3979664 | 52 | 4 [1] | [1] 2 | aslA/hemY | arylsulfatase AslA/protoheme IX biogenesis protein HemY |
* | * | ÷ | NZ_CP009273 | 4427375 | 4427430 | 56 | 4 [1] | [1] 4 | cysQ/BW25113_RS21900 | 3'(2'),5'‑bisphosphate nucleotidase CysQ/hypothetical protein |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 73 (3.940) | 32/168 | 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 = | 13 (0.700) | 17 (1.140) | 10/136 | 0.3 | 68.7% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 5 (0.330) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | 1686630 = | 5 (0.270) | 13 (0.710) | 3/166 | 1.7 | 72.5% | coding (479/1266 nt) | uidC | glucuronide uptake porin UidC |
? | NZ_CP009273 | 2095231 = | NA (NA) | intergenic (‑1/+145) | wbbL/BW25113_RS10605 | N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL/IS5‑like element IS5 family transposase | |||||
* | ? | NZ_CP009273 | = 1686634 | 6 (0.320) | 9 (0.490) | 8/168 | 0.7 | 60.0% | coding (475/1266 nt) | uidC | glucuronide uptake porin UidC |
? | 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 | = 1972751 | 0 (0.000) | 30 (1.620) | 14/168 | 0.3 | 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 = | 0 (0.000) | 3 (0.180) | 3/150 | 1.5 | 27.3% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | 4532813 = | 16 (0.970) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
* | ? | NZ_CP009273 | = 4532507 | 0 (0.000) | 4 (0.240) | 4/150 | 1.3 | 33.3% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | = 4532803 | 16 (0.970) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |