breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutation | |||||
---|---|---|---|---|---|
evidence | position | mutation | annotation | gene | description |
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 | 357570 | 590 | 3 [0] | [1] 2 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 380257 | 380274 | 18 | 3 [1] | [1] 2 | BW25113_RS01880/tauA | PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein |
* | * | ÷ | NZ_CP009273 | 418957 | 418994 | 38 | 2 [1] | [1] 2 | malZ | maltodextrin glucosidase |
* | * | ÷ | NZ_CP009273 | 428510 | 428585 | 76 | 2 [1] | [1] 3 | nrdR | transcriptional regulator NrdR |
* | * | ÷ | NZ_CP009273 | 579510 | 579597 | 88 | 2 [1] | [1] 2 | appY | DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 716391 | 716433 | 43 | 4 [0] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 729528 | 729552 | 25 | 3 [1] | [1] 2 | BW25113_RS03630 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 732255 | 732275 | 21 | 2 [1] | [1] 3 | ybfQ/BW25113_RS03650 | ISAs1 family transposase/ISAs1 family transposase |
* | * | ÷ | NZ_CP009273 | 733473–733501 | 733512 | 12–40 | 2 [1] | [1] 3 | BW25113_RS03650/ybfD | ISAs1 family transposase/ISAs1 family transposase |
* | * | ÷ | NZ_CP009273 | 806228 | 806235 | 8 | 2 [1] | [1] 2 | bioF | 8‑amino‑7‑oxononanoate synthase |
* | * | ÷ | NZ_CP009273 | 845800 | 845831 | 32 | 3 [0] | [1] 2 | BW25113_RS25505 | protein YliM |
* | * | ÷ | NZ_CP009273 | 886605 | 886615 | 11 | 3 [0] | [1] 3 | ybjC | DUF1418 family protein |
* | * | ÷ | NZ_CP009273 | 902712 | 902722 | 11 | 2 [1] | [1] 2 | ybjT | SDR family oxidoreductase |
* | * | ÷ | NZ_CP009273 | 993098 | 993137 | 40 | 3 [0] | [0] 2 | ssuE/elfA | NADPH‑dependent FMN reductase/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1136725 | 1136748 | 24 | 2 [0] | [1] 2 | rne | ribonuclease E |
* | * | ÷ | NZ_CP009273 | 1158254 | 1158289 | 36 | 2 [1] | [1] 3 | lpoB | penicillin‑binding protein activator LpoB |
* | * | ÷ | NZ_CP009273 | 1185151 | 1185166 | 16 | 3 [1] | [1] 2 | phoQ | two‑component system sensor histidine kinase PhoQ |
* | * | ÷ | NZ_CP009273 | 1210243 | 1210281 | 39 | 2 [1] | [1] 3 | bluF | blue light‑responsive regulator BluF |
* | * | ÷ | NZ_CP009273 | 1224991 | 1225003 | 13 | 2 [0] | [1] 3 | hlyE | hemolysin HlyE |
* | * | ÷ | NZ_CP009273 | 1267321 | 1267349 | 29 | 2 [1] | [1] 2 | chaA/chaB | sodium‑potassium/proton antiporter ChaA/putative cation transport regulator ChaB |
* | * | ÷ | NZ_CP009273 | 1281074 | 1281103 | 30 | 2 [1] | [1] 2 | narJ | nitrate reductase molybdenum cofactor assembly chaperone |
* | * | ÷ | NZ_CP009273 | 1287895 | 1287907 | 13 | 2 [1] | [0] 4 | galU/hns | UTP‑‑glucose‑1‑phosphate uridylyltransferase GalU/DNA‑binding transcriptional regulator H‑NS |
* | * | ÷ | NZ_CP009273 | 1320896 | 1320939 | 44 | 2 [1] | [1] 2 | [yciQ] | [yciQ] |
* | * | ÷ | NZ_CP009273 | 1327981 | 1327990 | 10 | 3 [0] | [1] 2 | topA/cysB | type I DNA topoisomerase/HTH‑type transcriptional regulator CysB |
* | * | ÷ | NZ_CP009273 | 1378896 | 1378921 | 26 | 2 [1] | [1] 4 | ycjX | YcjX family protein |
* | * | ÷ | NZ_CP009273 | 1379086 | 1379122 | 37 | 2 [1] | [1] 2 | ycjX | YcjX family protein |
* | * | ÷ | NZ_CP009273 | 1380929 | 1380980 | 52 | 3 [0] | [1] 4 | [tyrR] | [tyrR] |
* | * | ÷ | NZ_CP009273 | 1424178 | 1424226 | 49 | 2 [1] | [0] 2 | stfR | prophage tail fiber N‑terminal domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1424573 | 1424618 | 46 | 2 [1] | [1] 2 | stfR | prophage tail fiber N‑terminal domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1441322 | 1441337 | 16 | 2 [0] | [1] 2 | feaR | transcriptional regulator FeaR |
* | * | ÷ | NZ_CP009273 | 1446497 | 1446555 | 59 | 2 [1] | [1] 2 | paaZ | phenylacetic acid degradation bifunctional protein PaaZ |
* | * | ÷ | NZ_CP009273 | 1494752 | 1494776 | 25 | 2 [1] | [1] 2 | ydcK/tehA | YdcK family protein/dicarboxylate transporter/tellurite‑resistance protein TehA |
* | * | ÷ | NZ_CP009273 | 1499356 | 1499435 | 80 | 2 [1] | [1] 2 | ydcO | BenE family transporter YdcO |
* | * | ÷ | NZ_CP009273 | 1524590 | 1524600 | 11 | 2 [1] | [1] 3 | BW25113_RS26145 BW25113_RS25600 |
hypothetical protein protein YncO |
* | * | ÷ | NZ_CP009273 | 1540174 | 1540217 | 44 | 2 [1] | [0] 2 | yddL | porin |
* | * | ÷ | NZ_CP009273 | 1540271 | 1540468 | 198 | 2 [0] | [1] 2 | [yddL] | [yddL] |
* | * | ÷ | NZ_CP009273 | 1580810 | 1580836 | 27 | 2 [1] | [0] 2 | ydeP/ydeQ | acid resistance putative oxidoreductase YdeP/fimbrial protein |
* | * | ÷ | NZ_CP009273 | 1606397 | 1606402 | 6 | 2 [1] | [1] 2 | yneG | DUF4186 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1618892 | 1618930 | 39 | 2 [0] | [1] 2 | ydeI/ydeJ | YdeI family stress tolerance OB fold protein/2‑oxo‑tetronate isomerase |
* | * | ÷ | NZ_CP009273 | 1631300 | 1631313 | 14 | 2 [0] | [1] 2 | [ydfO] | [ydfO] |
* | * | ÷ | NZ_CP009273 | 1642474 | 1642474 | 1 | 4 [0] | [0] 2 | dicA | DNA‑binding transcriptional dual regulator DicA |
* | * | ÷ | NZ_CP009273 | 1663646 | 1663740 | 95 | 3 [1] | [1] 2 | ynfL | LysR family transcriptional regulator |
* | * | ÷ | NZ_CP009273 | 1680710 | 1680739 | 30 | 2 [1] | [1] 3 | fumC | class II fumarate hydratase |
* | * | ÷ | NZ_CP009273 | 1691816 | 1691816 | 1 | 2 [0] | [0] 2 | hdhA | 7‑alpha‑hydroxysteroid dehydrogenase |
* | * | ÷ | NZ_CP009273 | 1749652 | 1749668 | 17 | 2 [1] | [1] 2 | fumD/BW25113_RS26160 | fumarate hydratase FumD/protein YnhH |
* | * | ÷ | NZ_CP009273 | 1807091 | 1807208 | 118 | 3 [1] | [1] 2 | BW25113_RS09050 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1820594 | 1820604 | 11 | 3 [1] | [0] 2 | astE | succinylglutamate desuccinylase |
* | * | ÷ | NZ_CP009273 | 1864541 | 1864569 | 29 | 2 [0] | [1] 2 | yeaH/cdgI | YeaH/YhbH family protein/GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1887688 | 1887696 | 9 | 3 [1] | [1] 4 | yoaB | RidA family protein |
* | * | ÷ | NZ_CP009273 | 2052505 | 2052531 | 27 | 2 [1] | [1] 2 | yeeO | toxic metabolite efflux MATE transporter YeeO |
* | * | ÷ | NZ_CP009273 | 2100474 | 2100505 | 32 | 3 [1] | [1] 2 | wzy | O16 family O‑antigen polymerase |
* | * | ÷ | NZ_CP009273 | 2100676 | 2100714 | 39 | 3 [1] | [1] 2 | [wzy]–[glf] | [wzy],[glf] |
* | * | ÷ | NZ_CP009273 | 2146645 | 2146653 | 9 | 2 [1] | [0] 5 | yegL/ibsA | VWA domain‑containing protein/type I toxin‑antitoxin system toxin IbsA |
* | * | ÷ | NZ_CP009273 | 2149084 | 2149108 | 25 | 2 [1] | [1] 2 | mdtB | multidrug efflux RND transporter permease subunit MdtB |
* | * | ÷ | NZ_CP009273 | 2185861 | 2185918 | 58 | 2 [1] | [1] 2 | yehD/yehE | fimbrial protein/YehE family protein |
* | * | ÷ | NZ_CP009273 | 2249254 | 2249272 | 19 | 2 [1] | [1] 5 | yeiL | transcriptional regulator YeiL |
* | * | ÷ | NZ_CP009273 | 2345589 | 2345599 | 11 | 2 [0] | [1] 7 | glpT | glycerol‑3‑phosphate transporter |
* | * | ÷ | NZ_CP009273 | 2348065 | 2348087 | 23 | 2 [1] | [0] 2 | glpB | glycerol‑3‑phosphate dehydrogenase subunit GlpB |
* | * | ÷ | NZ_CP009273 | 2505253 | 2505277 | 25 | 2 [1] | [1] 2 | mntH | Nramp family divalent metal transporter |
* | * | ÷ | NZ_CP009273 | 2622990 | 2623002 | 13 | 2 [1] | [1] 2 | yfgG/yfgH | YfgG family protein/glycine zipper 2TM domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2672212 | 2672216 | 5 | 2 [0] | [0] 2 | yphF | substrate‑binding domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2696850 | 2696866 | 17 | 2 [1] | [0] 2 | rnc | ribonuclease III |
* | * | ÷ | NZ_CP009273 | 2779384 | 2779398 | 15 | 3 [0] | [1] 3 | BW25113_RS13825/BW25113_RS26005 | tRNA‑Ile/alpha‑amylase family glycosyl hydrolase |
* | * | ÷ | NZ_CP009273 | 2779845 | 2779881 | 37 | 2 [1] | [1] 2 | BW25113_RS26005 | alpha‑amylase family glycosyl hydrolase |
* | * | ÷ | NZ_CP009273 | 3576442 | 3576452 | 11 | 4 [0] | [1] 2 | BW25113_RS17825 | YrhA family protein |
* | * | ÷ | NZ_CP009273 | 4226572 | 4226594 | 23 | 3 [1] | [1] 2 | yjbF | YjbF family lipoprotein |
* | * | ÷ | NZ_CP009273 | 4344748 | 4344754 | 7 | 2 [0] | [1] 2 | lysS/dtpC | lysine‑‑tRNA ligase/dipeptide/tripeptide permease DtpC |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 60 (3.520) | 27/168 | 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 = | 11 (0.650) | 9 (0.650) | 9/136 | 0.3 | 51.6% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 8 (0.580) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 3 (0.180) | 3/166 | 1.4 | 37.8% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1972747 = | 5 (0.290) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |