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 | 1,613,627 | T→A | V84E (GTG→GAG) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
MC JC | 3,631,242 | Δ66 bp | coding (241‑306/1500 nt) | pitA → | inorganic phosphate transporter PitA |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356976 | 357570 | 595 | 2 [0] | [0] 4 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 380426 | 380467 | 42 | 2 [1] | [1] 2 | BW25113_RS01880/tauA | PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein |
* | * | ÷ | NZ_CP009273 | 385384 | 385416 | 33 | 2 [1] | [1] 2 | hemB/BW25113_RS01915 | porphobilinogen synthase/outer membrane autotransporter barrel domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 428529 | 428554 | 26 | 2 [0] | [1] 3 | nrdR | transcriptional regulator NrdR |
* | * | ÷ | NZ_CP009273 | 613496 | 613526 | 31 | 3 [1] | [0] 2 | entF/wzz(fepE) | enterobactin non‑ribosomal peptide synthetase EntF/LPS O‑antigen length regulator Wzz(fepE) |
* | * | ÷ | NZ_CP009273 | 651479 | 651500 | 22 | 2 [1] | [1] 2 | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP |
* | * | ÷ | NZ_CP009273 | 703464 | 703521 | 58 | 2 [1] | [1] 2 | glnS/chiP | glutamine‑‑tRNA ligase/chitoporin |
* | * | ÷ | NZ_CP009273 | 724884 | 724894 | 11 | 3 [1] | [0] 4 | ybfA/rhsC | YbfA family protein/rhs element protein RhsC |
* | * | ÷ | NZ_CP009273 | 733482 | 733509 | 28 | 2 [0] | [1] 3 | BW25113_RS03650/ybfD | ISAs1 family transposase/ISAs1 family transposase |
* | * | ÷ | NZ_CP009273 | 902983 | 903047 | 65 | 4 [1] | [1] 2 | ybjT | SDR family oxidoreductase |
* | * | ÷ | NZ_CP009273 | 950041 | 950059 | 19 | 2 [0] | [1] 3 | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
* | * | ÷ | NZ_CP009273 | 982534 | 982577 | 44 | 3 [1] | [1] 3 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 982691 | 982741 | 51 | 3 [1] | [1] 2 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 982919 | 982958 | 40 | 2 [0] | [1] 2 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 983061 | 983070 | 10 | 2 [1] | [0] 4 | asnS | asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 1088102 | 1088130 | 29 | 2 [1] | [1] 3 | pgaA/dgcT | poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1172301 | 1172357 | 57 | 3 [1] | [1] 2 | lolD | lipoprotein‑releasing ABC transporter ATP‑binding protein LolD |
* | * | ÷ | NZ_CP009273 | 1184942 | 1184959 | 18 | 2 [0] | [1] 2 | phoQ | two‑component system sensor histidine kinase PhoQ |
* | * | ÷ | NZ_CP009273 | 1193061 | 1193083 | 23 | 2 [1] | [1] 2 | BW25113_RS05920 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1207675 | 1207691 | 17 | 4 [0] | [0] 5 | iraM/BW25113_RS25985 | anti‑adapter protein IraM/protein YmgK |
* | * | ÷ | NZ_CP009273 | 1228934 | 1228942 | 9 | 3 [1] | [1] 2 | nhaB | Na(+)/H(+) antiporter NhaB |
* | * | ÷ | NZ_CP009273 | 1258706 | 1258784 | 79 | 3 [1] | [0] 6 | lolB | lipoprotein insertase outer membrane protein LolB |
* | * | ÷ | NZ_CP009273 | 1324129 | 1324151 | 23 | 2 [1] | [1] 4 | sohB | protease SohB |
* | * | ÷ | NZ_CP009273 | 1338988 | 1338990 | 3 | 2 [0] | [0] 2 | ymiD | protein YmiD |
* | * | ÷ | NZ_CP009273 | 1346015 | 1346061 | 47 | 2 [1] | [0] 2 | [ycjD] | [ycjD] |
* | * | ÷ | NZ_CP009273 | 1361224 | 1361236 | 13 | 2 [1] | [1] 4 | pspF | phage shock protein operon transcriptional activator |
* | * | ÷ | NZ_CP009273 | 1363718 | 1363754 | 37 | 3 [1] | [1] 2 | pspD | phage shock protein PspD |
* | * | ÷ | NZ_CP009273 | 1415759 | 1415783 | 25 | 2 [0] | [1] 3 | ydaU | YdaU family protein |
* | * | ÷ | NZ_CP009273 | 1459394 | 1459516 | 123 | 2 [1] | [1] 2 | BW25113_RS25580 | BW25113_RS25580 |
* | * | ÷ | NZ_CP009273 | 1521365 | 1521384 | 20 | 3 [1] | [1] 2 | yncH | YncH family protein |
* | * | ÷ | NZ_CP009273 | 1540297 | 1540372 | 76 | 2 [1] | [1] 2 | yddL/yddG | porin/aromatic amino acid efflux DMT transporter YddG |
* | * | ÷ | NZ_CP009273 | 1560574 | 1560652 | 79 | 3 [1] | [1] 4 | dosC | diguanylate cyclase DosC |
* | * | ÷ | NZ_CP009273 | 1572066 | 1572105 | 40 | 2 [1] | [1] 2 | yddA | ABC transporter ATP‑binding protein/permease |
* | * | ÷ | NZ_CP009273 | 1576961 | 1577049 | 89 | 2 [1] | [0] 3 | ydeN/ydeO | sulfatase/acid stress response transcriptional regulator YdeO |
* | * | ÷ | NZ_CP009273 | 1592526 | 1592543 | 18 | 2 [0] | [1] 3 | BW25113_RS07915/lsrK | ECSE_1600 family autotransporter/autoinducer‑2 kinase |
* | * | ÷ | NZ_CP009273 | 1729823 | 1729853 | 31 | 2 [0] | [1] 3 | sodB | superoxide dismutase [Fe] |
* | * | ÷ | NZ_CP009273 | 1826254 | 1826281 | 28 | 2 [0] | [1] 2 | astC/xthA | succinylornithine/acetylornithine transaminase/exodeoxyribonuclease III |
* | * | ÷ | NZ_CP009273 | 1830925 | 1830925 | 1 | 2 [0] | [0] 3 | ynjB | ABC transporter substrate‑binding protein |
* | * | ÷ | NZ_CP009273 | 1847216 | 1847226 | 11 | 2 [0] | [1] 3 | ydjE | MFS transporter |
* | * | ÷ | NZ_CP009273 | 1848410 | 1848429 | 20 | 2 [1] | [1] 2 | ydjF | DeoR/GlpR family DNA‑binding transcription regulator |
* | * | ÷ | NZ_CP009273 | 1864658 | 1864678 | 21 | 2 [1] | [1] 2 | cdgI | GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2096858 | 2096879 | 22 | 4 [1] | [1] 2 | [wbbL]–[wbbK] | [wbbL],[wbbK] |
* | * | ÷ | NZ_CP009273 | 2101613 | 2101623 | 11 | 2 [0] | [0] 2 | glf | UDP‑galactopyranose mutase |
* | * | ÷ | NZ_CP009273 | 2101895 | 2101916 | 22 | 2 [1] | [1] 2 | wzx | O16 family O‑antigen flippase |
* | * | ÷ | NZ_CP009273 | 2170689 | 2170764 | 76 | 2 [1] | [1] 2 | gatY/fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
* | * | ÷ | NZ_CP009273 | 2463182 | 2463192 | 11 | 4 [0] | [0] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2622990 | 2623030 | 41 | 3 [1] | [1] 2 | yfgG/yfgH | YfgG family protein/glycine zipper 2TM domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2897180 | 2897243 | 64 | 2 [1] | [1] 2 | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
* | * | ÷ | NZ_CP009273 | 2986924 | 2986952 | 29 | 2 [1] | [1] 3 | ygeH/BW25113_RS14840 | HilA family transcriptional regulator YgeH/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2988558 | 2988641 | 84 | 2 [1] | [1] 3 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2999279 | 2999304 | 26 | 2 [1] | [1] 2 | ygeV/ygeW | sigma‑54‑dependent Fis family transcriptional regulator/knotted carbamoyltransferase YgeW |
* | * | ÷ | NZ_CP009273 | 3129899 | 3129918 | 20 | 2 [0] | [1] 2 | pitB/gss | inorganic phosphate transporter PitB/bifunctional glutathionylspermidine amidase/synthase |
* | * | ÷ | NZ_CP009273 | 3178634 | 3178649 | 16 | 2 [0] | [0] 2 | ubiK/ygiL | ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein |
* | * | ÷ | NZ_CP009273 | 3262601 | 3262632 | 32 | 2 [1] | [1] 3 | yhaC | YhaC family protein |
* | * | ÷ | NZ_CP009273 | 3280620 | 3280634 | 15 | 2 [1] | [1] 2 | agaI/yraH | galactosamine‑6‑phosphate isomerase/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 3463406 | 3463433 | 28 | 2 [0] | [1] 2 | chiA/tuf | bifunctional chitinase/lysozyme/elongation factor Tu |
* | * | ÷ | NZ_CP009273 | 3647059 | 3647077 | 19 | 5 [1] | [0] 3 | BW25113_RS18165/slp | hypothetical protein/outer membrane lipoprotein Slp |
* | * | ÷ | NZ_CP009273 | 3837241 | 3837296 | 56 | 3 [1] | [1] 2 | adeQ/adeD | adenine permease AdeQ/adenine deaminase |
* | * | ÷ | NZ_CP009273 | 4241449 | 4241450 | 2 | 3 [0] | [0] 3 | BW25113_RS20970 | SopA family protein |
* | * | ÷ | NZ_CP009273 | 4466835 | 4466882 | 48 | 2 [0] | [0] 2 | BW25113_RS22080 | hypothetical protein |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 15391 = | NA (NA) | 19 (1.010) | 14/156 | 0.3 | 95.2% | intergenic (+93/‑54) | dnaJ/BW25113_RS00080 | molecular chaperone DnaJ/IS4‑like element IS421 family transposase |
? | NZ_CP009273 | = 454255 | 1 (0.050) | intergenic (+99/‑89) | clpX/lon | ATP‑dependent protease ATP‑binding subunit ClpX/endopeptidase La | |||||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 28 (1.410) | 16/164 | 0.2 | 40.6% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
? | NZ_CP009273 | = 360286 | 41 (2.070) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
* | ? | NZ_CP009273 | 454243 = | 3 (0.150) | 21 (1.100) | 14/158 | 0.3 | 87.9% | intergenic (+87/‑101) | clpX/lon | ATP‑dependent protease ATP‑binding subunit ClpX/endopeptidase La |
? | NZ_CP009273 | = 604803 | NA (NA) | intergenic (+170/+112) | BW25113_RS03025/entD | IS4‑like element IS421 family transposase/enterobactin synthase subunit EntD | |||||
* | ? | NZ_CP009273 | 1203246 = | 0 (0.000) | 8 (0.500) | 8/132 | 0.5 | 94.1% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 1 (0.060) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1203261 | 0 (0.000) | 7 (0.440) | 6/132 | 0.7 | 93.3% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | = 1205058 | 1 (0.060) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 8 (0.410) | 6/162 | 1.0 | 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) | 21 (1.060) | 12/164 | 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 | |||||
* | ? | NZ_CP009273 | 4532499 = | 1 (0.050) | 11 (0.620) | 8/146 | 0.6 | 81.8% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | 4532813 = | 4 (0.230) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
* | ? | NZ_CP009273 | = 4532507 | 1 (0.050) | 7 (0.400) | 6/146 | 0.8 | 74.1% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | = 4532803 | 4 (0.230) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |