mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 2,719,426 | T→C | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 4,173,025 | A→T | Q618L (CAG→CTG) | rpoB → | RNA polymerase, beta subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 403343 | 403366 | 24 | 3 [1] | [1] 2 | aroM | AroM family protein |
| * | * | ÷ | CP009273 | 414985 | 415038 | 54 | 3 [1] | [1] 3 | phoR/brnQ | sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| * | * | ÷ | CP009273 | 518493 | 518506 | 14 | 3 [0] | [0] 3 | ybbP/rhsD | putative ABC transporter permease/Rhs family putative polymorphic toxin |
| * | * | ÷ | CP009273 | 716119 | 716121 | 3 | 4 [0] | [1] 3 | ybfK | uncharacterized protein |
| * | * | ÷ | CP009273 | 1000524 | 1000525 | 2 | 2 [0] | [0] 2 | pyrD | dihydro‑orotate oxidase, FMN‑linked |
| * | * | ÷ | CP009273 | 1084425 | 1084438 | 14 | 3 [0] | [1] 2 | pgaB | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| * | * | ÷ | CP009273 | 1385460 | 1385526 | 67 | 2 [1] | [0] 6 | ycjY | S9 homolog non‑peptidase family protein |
| * | * | ÷ | CP009273 | 1485206 | 1485225 | 20 | 2 [0] | [0] 5 | cybB | cytochrome b561 |
| * | * | ÷ | CP009273 | 1493044 | 1493051 | 8 | 2 [0] | [0] 4 | ydcH | DUF465 family protein |
| * | * | ÷ | CP009273 | 1524310 | 1524473 | 164 | 7 [1] | [1] 3 | ydcD | uncharacterized protein |
| * | * | ÷ | CP009273 | 1800398 | 1800470 | 73 | 2 [1] | [1] 2 | ydiY/pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| * | * | ÷ | CP009273 | 1850968 | 1851013 | 46 | 2 [1] | [0] 4 | ydjH | putative kinase |
| * | * | ÷ | CP009273 | 1990311 | 1990401 | 91 | 2 [1] | [0] 2 | [sdiA] | [sdiA] |
| * | * | ÷ | CP009273 | 2027279 | 2027451 | 173 | 2 [1] | [0] 2 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2099577 | 2099607 | 31 | 2 [1] | [0] 2 | wbbH | O‑antigen polymerase |
| * | * | ÷ | CP009273 | 2128155 | 2128197 | 43 | 3 [0] | [1] 6 | wzc | colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase |
| * | * | ÷ | CP009273 | 2462908 | 2462922 | 15 | 2 [0] | [1] 3 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2767748 | 2767851 | 104 | 3 [1] | [1] 2 | yfjW | CP4‑57 prophage; putative inner membrane protein |
| * | * | ÷ | CP009273 | 3256094 | 3256114 | 21 | 2 [1] | [1] 2 | tdcD | propionate kinase/acetate kinase C, anaerobic |
| * | * | ÷ | CP009273 | 3277435 | 3277457 | 23 | 3 [1] | [1] 2 | kbaY/agaB | tagatose 6‑phosphate aldolase 1, kbaY subunit/N‑acetylgalactosamine‑specific enzyme IIB component of PTS |
| * | * | ÷ | CP009273 | 3406911 | 3406961 | 51 | 2 [1] | [0] 4 | acrS/acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| * | * | ÷ | CP009273 | 3432084 | 3432173 | 90 | 2 [1] | [1] 2 | zntR | zntA gene transcriptional activator |
| * | * | ÷ | CP009273 | 3432314 | 3432495 | 182 | 2 [1] | [1] 3 | [zntR] | [zntR] |
| * | * | ÷ | CP009273 | 3787045 | 3787082 | 38 | 3 [0] | [0] 2 | yibB/hldD | YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding |
| * | * | ÷ | CP009273 | 4294328 | 4294380 | 53 | 2 [1] | [1] 2 | ytcA/yjcS | putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein |
| * | * | ÷ | CP009273 | 4561788 | 4561836 | 49 | 2 [1] | [1] 5 | yjiS/yjiT | DUF1127 family protein/pseudogene |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 18 (0.940) | 24 (1.260) | 16/268 | 0.1 | 57.1% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 896205 = | NA (NA) | 4 (0.240) | 4/232 | 1.0 | 22.2% | noncoding (1/87 nt) | REP83 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP83 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | CP009273 | = 4604174 | 14 (0.850) | noncoding (101/388 nt) | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | |||||
| * | ? | CP009273 | = 1046001 | 12 (0.630) | 35 (1.830) | 16/268 | 0.1 | 83.3% | intergenic (+15/+418) | insB1/cspH | IS1 transposase B/stress protein, member of the CspA‑family |
| ? | CP009273 | = 1972861 | 2 (0.100) | intergenic (‑407/‑373) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 4 (0.210) | 10 (0.590) | 8/236 | 0.5 | 70.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 5 (0.300) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 4 (0.210) | 9 (0.540) | 4/236 | 1.0 | 67.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 5 (0.300) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972854 = | 6 (0.310) | 17 (0.890) | 9/268 | 0.5 | 73.9% | intergenic (‑400/‑380) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 3939403 | 6 (0.310) | 3 (0.160) | 3/260 | 1.4 | 34.0% | noncoding (2340/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | CP009273 | 4033298 = | NA (NA) | noncoding (2420/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||