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 | 427,415 | Δ2 bp | coding (54‑55/885 nt) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
RA | 690,117 | C→T | V99I (GTC→ATC) | miaB ← | tRNA (N6‑isopentenyl adenosine(37)‑C2)‑methylthiotransferase MiaB |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
JC | 4,609,810 | Δ72 bp | coding (391‑462/1224 nt) | deoB → | phosphopentomutase |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356981 | 357574 | 594 | 2 [0] | [1] 3 | [lacA] | [lacA] |
* | * | ÷ | NZ_CP009273 | 370665 | 370757–370716 | 52–93 | 3 [1] | [1] 4 | dmpG/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑(3‑hydroxy‑phenyl)propionate transporter |
* | * | ÷ | NZ_CP009273 | 396670 | 396680 | 11 | 2 [0] | [1] 2 | BW25113_RS25915/iraP | hypothetical protein/anti‑adapter protein IraP |
* | * | ÷ | NZ_CP009273 | 414663 | 414678 | 16 | 2 [1] | [0] 2 | phoR/brnQ | phosphate regulon sensor histidine kinase PhoR/branched‑chain amino acid transporter carrier protein BrnQ |
* | * | ÷ | NZ_CP009273 | 437903 | 437912 | 10 | 2 [1] | [0] 2 | thiI | tRNA 4‑thiouridine(8) synthase ThiI |
* | * | ÷ | NZ_CP009273 | 564255 | 564281 | 27 | 3 [0] | [1] 2 | BW25113_RS25485 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 579573 | 579588 | 16 | 4 [1] | [1] 2 | appY | DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 608874 | 608901 | 28 | 2 [1] | [1] 2 | fes | enterochelin esterase |
* | * | ÷ | NZ_CP009273 | 642167 | 642246 | 80 | 2 [0] | [0] 2 | citG | triphosphoribosyl‑dephospho‑CoA synthase CitG |
* | * | ÷ | NZ_CP009273 | 656058 | 656076 | 19 | 2 [1] | [1] 2 | ybeF | YbeF family transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 725196 | 725208–725204 | 9–13 | 2 [1] | [0] 3 | rhsC | rhs element protein RhsC |
* | * | ÷ | NZ_CP009273 | 774498 | 774533 | 36 | 2 [1] | [0] 3 | [pal] | [pal] |
* | * | ÷ | NZ_CP009273 | 803725 | 803821 | 97 | 2 [1] | [1] 2 | bioA | adenosylmethionine‑‑8‑amino‑7‑oxononanoate transaminase |
* | * | ÷ | NZ_CP009273 | 830786 | 830798 | 13 | 2 [1] | [1] 3 | ybiB | DNA‑binding protein YbiB |
* | * | ÷ | NZ_CP009273 | 836284 | 836353 | 70 | 2 [1] | [1] 2 | fiu | catecholate siderophore receptor Fiu |
* | * | ÷ | NZ_CP009273 | 839633 | 839658 | 26 | 2 [0] | [0] 2 | ybiO | mechanosensitive channel protein |
* | * | ÷ | NZ_CP009273 | 859429 | 859498 | 70 | 2 [1] | [1] 3 | fsa | fructose‑6‑phosphate aldolase |
* | * | ÷ | NZ_CP009273 | 885077 | 885103 | 27 | 2 [1] | [1] 2 | ybjL | aspartate:alanine antiporter |
* | * | ÷ | NZ_CP009273 | 969791 | 969854 | 64 | 2 [1] | [1] 2 | mukF | chromosome partition protein MukF |
* | * | ÷ | NZ_CP009273 | 988185 | 988231 | 47 | 2 [1] | [1] 3 | pepN | aminopeptidase N |
* | * | ÷ | NZ_CP009273 | 988405 | 988441 | 37 | 3 [1] | [1] 2 | pepN | aminopeptidase N |
* | * | ÷ | NZ_CP009273 | 988565 | 988582 | 18 | 2 [1] | [1] 4 | pepN | aminopeptidase N |
* | * | ÷ | NZ_CP009273 | 990973 | 990987 | 15 | 2 [1] | [1] 2 | ssuD | FMNH2‑dependent alkanesulfonate monooxygenase |
* | * | ÷ | NZ_CP009273 | 998257 | 998270 | 14 | 2 [1] | [1] 2 | elfG | fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1003088 | 1003106 | 19 | 2 [1] | [1] 2 | ycbX/rlmKL | 6‑N‑hydroxylaminopurine resistance protein YcbX/bifunctional 23S rRNA (guanine(2069)‑N(7))‑methyltransferase RlmK/23S rRNA (guanine(2445)‑N(2))‑methyltransferase RlmL |
* | * | ÷ | NZ_CP009273 | 1070848 | 1070868 | 21 | 2 [0] | [1] 2 | putA | trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase |
* | * | ÷ | NZ_CP009273 | 1074796 | 1074870 | 75 | 3 [1] | [1] 3 | putP | sodium/proline symporter PutP |
* | * | ÷ | NZ_CP009273 | 1080297 | 1080341 | 45 | 2 [1] | [1] 2 | efeB/phoH | iron uptake transporter deferrochelatase/peroxidase subunit/phosphate starvation‑inducible protein PhoH |
* | * | ÷ | NZ_CP009273 | 1088349 | 1088360 | 12 | 2 [1] | [0] 2 | dgcT | GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1100140 | 1100200 | 61 | 2 [1] | [1] 2 | csgA | curli major subunit CsgA |
* | * | ÷ | NZ_CP009273 | 1115826 | 1115855 | 30 | 2 [1] | [1] 2 | solA | N‑methyl‑L‑tryptophan oxidase |
* | * | ÷ | NZ_CP009273 | 1139930 | 1139933 | 4 | 2 [0] | [1] 2 | rne/rluC | ribonuclease E/23S rRNA pseudouridine(955/2504/2580) synthase RluC |
* | * | ÷ | NZ_CP009273 | 1168434 | 1168442 | 9 | 2 [1] | [1] 2 | mfd | transcription‑repair coupling factor |
* | * | ÷ | NZ_CP009273 | 1172115 | 1172234 | 120 | 2 [1] | [1] 2 | lolD | lipoprotein‑releasing ABC transporter ATP‑binding protein LolD |
* | * | ÷ | NZ_CP009273 | 1173161 | 1173169 | 9 | 2 [0] | [1] 2 | lolE | lipoprotein‑releasing ABC transporter permease subunit LolE |
* | * | ÷ | NZ_CP009273 | 1178465 | 1178493 | 29 | 3 [0] | [0] 3 | potC | spermidine/putrescine ABC transporter permease PotC |
* | * | ÷ | NZ_CP009273 | 1192488 | 1192534 | 47 | 2 [1] | [0] 3 | ymfD | class I SAM‑dependent methyltransferase |
* | * | ÷ | NZ_CP009273 | 1206653 | 1206676 | 24 | 3 [1] | [1] 2 | mcrA/BW25113_RS23640 | 5‑methylcytosine‑specific endonuclease McrA/isocitrate/isopropylmalate family dehydrogenase |
* | * | ÷ | NZ_CP009273 | 1207640 | 1207691 | 52 | 2 [1] | [1] 2 | iraM/BW25113_RS25985 | anti‑adapter protein IraM/protein YmgK |
* | * | ÷ | NZ_CP009273 | 1210191 | 1210207 | 17 | 2 [1] | [1] 2 | bluF | blue light‑responsive regulator BluF |
* | * | ÷ | NZ_CP009273 | 1210566 | 1210612 | 47 | 2 [1] | [1] 2 | bluF | blue light‑responsive regulator BluF |
* | * | ÷ | NZ_CP009273 | 1229158 | 1229164 | 7 | 4 [0] | [1] 2 | nhaB | Na(+)/H(+) antiporter NhaB |
* | * | ÷ | NZ_CP009273 | 1264246 | 1264348 | 103 | 2 [1] | [1] 2 | kdsA | 3‑deoxy‑8‑phosphooctulonate synthase |
* | * | ÷ | NZ_CP009273 | 1269200 | 1269204 | 5 | 2 [0] | [1] 2 | ychN/ychO | DsrE/F sulfur relay family protein YchN/inverse autotransporter invasin YchO |
* | * | ÷ | NZ_CP009273 | 1275040 | 1275071 | 32 | 2 [1] | [1] 2 | narK/narG | nitrate transporter NarK/nitrate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 1277039 | 1277059 | 21 | 2 [1] | [1] 2 | narG | nitrate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 1277150 | 1277210 | 61 | 2 [1] | [1] 2 | narG | nitrate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 1279571 | 1279602 | 32 | 2 [1] | [1] 2 | narH | nitrate reductase subunit beta |
* | * | ÷ | NZ_CP009273 | 1285411 | 1285422 | 12 | 2 [1] | [1] 2 | rssA | patatin‑like phospholipase RssA |
* | * | ÷ | NZ_CP009273 | 1310589 | 1310651 | 63 | 3 [0] | [1] 2 | yciG/trpA | general stress protein/tryptophan synthase subunit alpha |
* | * | ÷ | NZ_CP009273 | 1314944 | 1314981 | 38 | 2 [1] | [1] 2 | trpD | bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD |
* | * | ÷ | NZ_CP009273 | 1326825 | 1326889 | 65 | 2 [0] | [1] 2 | topA | type I DNA topoisomerase |
* | * | ÷ | NZ_CP009273 | 1347681 | 1347689 | 9 | 2 [0] | [1] 2 | sapD | peptide ABC transporter ATP‑binding protein SapD |
* | * | ÷ | NZ_CP009273 | 1356397 | 1356412 | 16 | 2 [1] | [0] 2 | puuR | HTH‑type transcriptional regulator PuuR |
* | * | ÷ | NZ_CP009273 | 1369129 | 1369145 | 17 | 2 [1] | [0] 2 | ycjP | carbohydrate ABC transporter permease |
* | * | ÷ | NZ_CP009273 | 1369423 | 1369451 | 29 | 2 [1] | [1] 2 | ycjQ | zinc‑binding alcohol dehydrogenase |
* | * | ÷ | NZ_CP009273 | 1393448 | 1393453 | 6 | 2 [1] | [0] 2 | fnr | fumarate/nitrate reduction transcriptional regulator Fnr |
* | * | ÷ | NZ_CP009273 | 1398225 | 1398233 | 9 | 2 [0] | [1] 2 | abgA | p‑aminobenzoyl‑glutamate hydrolase subunit AbgA |
* | * | ÷ | NZ_CP009273 | 1417984 | 1418005 | 22 | 2 [1] | [1] 2 | BW25113_RS26130/trkG | hypothetical protein/Trk system potassium transporter TrkG |
* | * | ÷ | NZ_CP009273 | 1632746 | 1632782 | 37 | 2 [1] | [1] 2 | cspI | cold shock protein CspI |
* | * | ÷ | NZ_CP009273 | 1733854 | 1733896 | 43 | 2 [1] | [1] 2 | punR | DNA‑binding transcriptional activator PunR |
* | * | ÷ | NZ_CP009273 | 1781854 | 1781858 | 5 | 2 [1] | [0] 2 | ppsR | posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
* | * | ÷ | NZ_CP009273 | 2005763 | 2005774 | 12 | 2 [1] | [0] 2 | BW25113_RS10120 | DUF5503 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2753605 | 2753686 | 82 | 2 [1] | [1] 3 | yfjI | YfjI family protein |
* | * | ÷ | NZ_CP009273 | 2768289 | 2768291 | 3 | 3 [0] | [0] 3 | BW25113_RS13770 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3575397 | 3575430 | 34 | 9 [0] | [1] 2 | hcp | Hcp1 family type VI secretion system effector |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 43 (2.670) | 28/168 | 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 = | 1 (0.060) | 7 (0.540) | 7/136 | 0.5 | 83.3% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 2 (0.150) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 7 (0.440) | 6/166 | 0.8 | 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) | 19 (1.180) | 13/168 | 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 | 4532499 = | 7 (0.440) | 6 (0.420) | 6/150 | 0.7 | 26.5% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | 4532813 = | 27 (1.880) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |