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 | 49,898 | G→A | A26T (GCC→ACC) | folA → | type 3 dihydrofolate reductase |
RA | 49,910 | T→G | W30G (TGG→GGG) | folA → | type 3 dihydrofolate reductase |
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 | 356981 | 357567 | 587 | 11 [0] | [0] 2 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 380369 | 380389 | 21 | 2 [0] | [0] 2 | BW25113_RS01880/tauA | PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein |
* | * | ÷ | NZ_CP009273 | 578986 | 579017 | 32 | 2 [0] | [0] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 651715 | 651732 | 18 | 2 [1] | [1] 3 | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP |
* | * | ÷ | NZ_CP009273 | 716396 | 716436 | 41 | 3 [1] | [0] 4 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 766297 | 766353 | 57 | 2 [1] | [1] 2 | mngB/cydA | mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I |
* | * | ÷ | NZ_CP009273 | 982718 | 982728 | 11 | 3 [0] | [0] 5 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 993098 | 993107 | 10 | 4 [0] | [0] 2 | ssuE/elfA | NADPH‑dependent FMN reductase/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 993889 | 993914 | 26 | 2 [0] | [1] 5 | elfA/elfD | fimbrial protein/molecular chaperone |
* | * | ÷ | NZ_CP009273 | 1098624 | 1098632 | 9 | 2 [0] | [1] 3 | csgD | biofilm master transcriptional regulator CsgD |
* | * | ÷ | NZ_CP009273 | 1192704 | 1192714 | 11 | 3 [0] | [1] 2 | ymfD | class I SAM‑dependent methyltransferase |
* | * | ÷ | NZ_CP009273 | 1193247 | 1193279 | 33 | 3 [1] | [1] 2 | BW25113_RS05920 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1193517 | 1193541 | 25 | 2 [0] | [0] 2 | BW25113_RS05920 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1212066 | 1212121 | 56 | 2 [0] | [1] 3 | [ariR] | [ariR] |
* | * | ÷ | NZ_CP009273 | 1215785 | 1215804 | 20 | 3 [0] | [0] 4 | BW25113_RS25990 | autotransporter outer membrane beta‑barrel domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1389983 | 1390012 | 30 | 2 [1] | [1] 4 | ynaI | low conductance mechanosensitive channel YnaI |
* | * | ÷ | NZ_CP009273 | 1459449 | 1459516 | 68 | 2 [1] | [1] 2 | [BW25113_RS25580] | [BW25113_RS25580] |
* | * | ÷ | NZ_CP009273 | 1521302 | 1521332 | 31 | 2 [0] | [1] 4 | yncH | YncH family protein |
* | * | ÷ | NZ_CP009273 | 1539082 | 1539082 | 1 | 2 [0] | [0] 2 | BW25113_RS07710 | leucine‑rich repeat domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1539476 | 1539509 | 34 | 3 [1] | [1] 2 | BW25113_RS07710 | leucine‑rich repeat domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1631762 | 1631762 | 1 | 2 [0] | [0] 2 | ydfO/gnsB | DUF1398 domain‑containing protein/addiction module toxin, GnsA/GnsB family |
* | * | ÷ | NZ_CP009273 | 1635012 | 1635032 | 21 | 2 [0] | [1] 2 | essD/ynfU | phage lysis protein EssD/putative zinc‑binding protein YnfU |
* | * | ÷ | NZ_CP009273 | 1783823 | 1783859 | 37 | 2 [1] | [1] 2 | aroH/hemP | 3‑deoxy‑7‑phosphoheptulonate synthase AroH/hemin uptake protein HemP |
* | * | ÷ | NZ_CP009273 | 1797615 | 1797667 | 53 | 2 [1] | [1] 4 | espL1 | type III secretion system effector EspL1 |
* | * | ÷ | NZ_CP009273 | 2027309 | 2027321 | 13 | 3 [0] | [0] 2 | drpB/ompC | cell division protein DrpB/porin OmpC |
* | * | ÷ | NZ_CP009273 | 2050181 | 2050258 | 78 | 2 [0] | [1] 2 | amn/yeeN | AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 2098708 | 2098732 | 25 | 5 [1] | [0] 2 | wbbI | beta‑1,6‑galactofuranosyltransferase |
* | * | ÷ | NZ_CP009273 | 2101634 | 2101651 | 18 | 2 [1] | [0] 2 | glf | UDP‑galactopyranose mutase |
* | * | ÷ | NZ_CP009273 | 2185829 | 2185901 | 73 | 2 [0] | [1] 2 | yehD/yehE | fimbrial protein/YehE family protein |
* | * | ÷ | NZ_CP009273 | 2463798 | 2463839 | 42 | 2 [1] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2569339 | 2569349 | 11 | 2 [1] | [0] 3 | eutS/maeB | ethanolamine utilization microcompartment protein EutS/NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase |
* | * | ÷ | NZ_CP009273 | 2779644 | 2779670 | 27 | 2 [0] | [1] 2 | BW25113_RS13825/BW25113_RS26005 | tRNA‑Ile/alpha‑amylase family glycosyl hydrolase |
* | * | ÷ | NZ_CP009273 | 2781142 | 2781142 | 1 | 5 [0] | [0] 3 | BW25113_RS26005 | alpha‑amylase family glycosyl hydrolase |
* | * | ÷ | NZ_CP009273 | 2782042 | 2782065 | 24 | 4 [1] | [0] 2 | BW25113_RS26005/csiD | alpha‑amylase family glycosyl hydrolase/glutarate dioxygenase GlaH |
* | * | ÷ | NZ_CP009273 | 2877604 | 2877607 | 4 | 2 [0] | [0] 2 | casA/cas3 | type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3 |
* | * | ÷ | NZ_CP009273 | 2877759 | 2877791 | 33 | 2 [1] | [1] 3 | casA/cas3 | type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3 |
* | * | ÷ | NZ_CP009273 | 3492786 | 3492794 | 9 | 2 [0] | [0] 2 | cysG/yhfL | siroheme synthase CysG/YhfL family protein |
* | * | ÷ | NZ_CP009273 | 3763096 | 3763128 | 33 | 2 [1] | [1] 3 | BW25113_RS26240 | Imm57 family immunity protein |
* | * | ÷ | NZ_CP009273 | 4258927 | 4258938 | 12 | 2 [0] | [1] 3 | BW25113_RS26020 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 4561743 | 4561802 | 60 | 10 [1] | [1] 2 | yjiS/yjiT | DUF1127 domain‑containing protein/protein YjiT |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | = 270581 | NA (NA) | 3 (0.100) | 3/150 | 2.2 | NA | coding (212/981 nt) | BW25113_RS01325 | IS5‑like element IS5 family transposase |
? | NZ_CP009273 | = 270584 | NA (NA) | coding (209/981 nt) | BW25113_RS01325 | IS5‑like element IS5 family transposase | |||||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 93 (3.010) | 40/156 | 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 = | 29 (0.940) | 5 (0.200) | 5/124 | 1.4 | 25.0% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 7 (0.280) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 11 (0.360) | 7/154 | 1.4 | 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) | 26 (0.840) | 17/156 | 0.4 | 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 |