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 | 1,242,915 | A→C | intergenic (‑83/+237) | treA ← / ← dhaM | periplasmic trehalase/putative dihydroxyacetone‑specific PTS enzymes: HPr component/EI component |
| RA | 2,719,426 | T→C | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 578901 | 579034 | 134 | 6 [1] | [0] 4 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | CP009273 | 1251939 | 1251951 | 13 | 3 [0] | [2] 4 | ycgV/ychF | putative adhesin/catalase inhibitor protein; ATPase, K+‑dependent, ribosome‑associated |
| * | * | ÷ | CP009273 | 1435245 | 1435267 | 23 | 3 [2] | [2] 3 | pfo/ydbJ | pyruvate‑flavodoxin oxidoreductase/DUF333 family putative lipoprotein |
| * | * | ÷ | CP009273 | 1524292 | 1524445 | 154 | 3 [2] | [2] 3 | ydcD | uncharacterized protein |
| * | * | ÷ | CP009273 | 1635190 | 1635351 | 162 | 3 [1] | [2] 3 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock protein |
| * | * | ÷ | CP009273 | 1725479 | 1725587 | 109 | 3 [2] | [2] 6 | lhr | putative ATP‑dependent helicase |
| * | * | ÷ | CP009273 | 1990357 | 1990431 | 75 | 3 [2] | [1] 3 | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC superfamily transporter ATP‑binding subunit |
| * | * | ÷ | CP009273 | 3432038 | 3432495 | 458 | 4 [2] | [2] 3 | zntR | zntR |
| * | * | ÷ | CP009273 | 3448800 | 3448837 | 38 | 3 [2] | [0] 3 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | CP009273 | 3575223 | 3575288 | 66 | 3 [2] | [2] 3 | yhhZ | putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity |
| * | * | ÷ | CP009273 | 3745304 | 3745331 | 28 | 4 [1] | [0] 4 | yiaT/yiaU | putative outer membrane protein/putative DNA‑binding transcriptional regulator |
| * | * | ÷ | CP009273 | 4294346 | 4294410 | 65 | 4 [0] | [2] 3 | ytcA/yjcS | putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 287112 | NA (NA) | 18 (0.810) | 14/266 | 0.3 | 69.4% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | CP009273 | 1972854 = | 8 (0.360) | intergenic (‑400/‑380) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 360104 = | 23 (1.030) | 27 (1.200) | 17/268 | 0.2 | 54.0% | 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 | 1203246 = | 10 (0.450) | 10 (0.510) | 10/236 | 0.5 | 61.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 4 (0.200) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 10 (0.450) | 15 (0.760) | 12/236 | 0.3 | 70.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 4 (0.200) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1972861 | 6 (0.270) | 35 (1.560) | 20/268 | 0.1 | 85.4% | intergenic (‑407/‑373) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | 2166630 = | 15 (0.670) | 3 (0.220) +51 bp |
3/166 | 1.2 | 24.4% | coding (1128/1356 nt) | gatC | galactitol PTS permease ‑ GatC subunit |
| ? | CP009273 | = 2514487 | 15 (0.670) | noncoding (215/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | = 4178728 | 23 (1.060) | 10 (0.460) +AAG |
6/254 | 1.1 | 30.5% | coding (3451/4224 nt) | rpoC | RNA polymerase, beta prime subunit |
| ? | CP009273 | 4178729 = | 23 (1.030) | coding (3452/4224 nt) | rpoC | RNA polymerase, beta prime subunit | |||||
| * | ? | CP009273 | 4363113 = | 32 (1.530) | 15 (0.720) | 3/248 | 1.8 | 32.1% | intergenic (+134/+69) | yjeI/yjeJ | DUF4156 family lipoprotein/uncharacterized protein |
| ? | CP009273 | 4364315 = | NA (NA) | noncoding (1/99 nt) | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||