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 | 749,443 | G→A | A161V (GCC→GTC) | gltA ← | citrate synthase |
MC JC | 1,605,880 | Δ9,701 bp | [yneF]–eamA | [yneF], yneG, glsB, sad, yneJ, yneK, ydeA, marC, marR, marA, marB, eamA | |
RA | 4,029,087 | A→T | noncoding (197/1542 nt) | rrsA → | 16S ribosomal RNA of rrnA operon |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | CP009273 | 80475 | 80684 | 210 | 8 [6] | [7] 8 | leuL/leuO | leu operon leader peptide/global transcription factor |
* | * | ÷ | CP009273 | 290523 | 290658 | 136 | 9 [7] | [7] 9 | yagM/yagN | CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein |
* | * | ÷ | CP009273 | 295775 | 295852 | 78 | 8 [7] | [7] 8 | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
* | * | ÷ | CP009273 | 729480 | 729604 | 125 | 13 [6] | [7] 8 | [ybfB]–[rhsO] | [ybfB],[rhsO] |
* | * | ÷ | CP009273 | 808453 | 808638 | 186 | 8 [7] | [7] 9 | bioD/uvrB | dethiobiotin synthetase/excinulease of nucleotide excision repair, DNA damage recognition component |
* | * | ÷ | CP009273 | 1192947 | 1193323 | 377 | 8 [6] | [7] 9 | [ymfD]–[ymfE] | [ymfD],[ymfE] |
* | * | ÷ | CP009273 | 1207350 | 1207965 | 616 | 9 [7] | [7] 9 | [iraM] | [iraM] |
* | * | ÷ | CP009273 | 1524229 | 1524695 | 467 | 8 [6] | [6] 8 | [ydcD] | [ydcD] |
* | * | ÷ | CP009273 | 1972847 | 1972922 | 76 | 9 [7] | [6] 8 | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
* | * | ÷ | CP009273 | 1981893 | 1982202 | 310 | 10 [7] | [7] 8 | [yecR]–[ftnA] | [yecR],[ftnA] |
* | * | ÷ | CP009273 | 2050156 | 2050300 | 145 | 8 [7] | [7] 9 | amn/yeeN | AMP nucleosidase/UPF0082 family protein |
* | * | ÷ | CP009273 | 2096855 | 2097103 | 249 | 11 [7] | [7] 9 | [wbbL]–[wbbK] | [wbbL],[wbbK] |
* | * | ÷ | CP009273 | 2097172 | 2097625 | 454 | 9 [7] | [6] 8 | wbbK | lipopolysaccharide biosynthesis protein |
* | * | ÷ | CP009273 | 2099526 | 2099759 | 234 | 9 [6] | [7] 9 | [wbbI]–[wbbH] | [wbbI],[wbbH] |
* | * | ÷ | CP009273 | 2144425 | 2144594 | 170 | 8 [7] | [5] 8 | [yegI] | [yegI] |
* | * | ÷ | CP009273 | 2462758 | 2463234 | 477 | 11 [7] | [6] 8 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
* | * | ÷ | CP009273 | 2768211 | 2768465 | 255 | 12 [6] | [6] 8 | [yfjW] | [yfjW] |
* | * | ÷ | CP009273 | 2790481 | 2790582 | 102 | 8 [7] | [7] 8 | [ygaV] | [ygaV] |
* | * | ÷ | CP009273 | 2798140 | 2798330 | 191 | 8 [6] | [7] 9 | [proV] | [proV] |
* | * | ÷ | CP009273 | 2897078 | 2897265 | 188 | 8 [7] | [5] 8 | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
* | * | ÷ | CP009273 | 2975660 | 2975792 | 133 | 9 [7] | [7] 11 | araE/kduD | arabinose transporter/hexuronate dehydrogenase; hexuronate utilization in high osmolarity |
* | * | ÷ | CP009273 | 2988524 | 2988838 | 315 | 9 [5] | [6] 8 | [ygeN] | [ygeN] |
* | * | ÷ | CP009273 | 2988962 | 2989393 | 432 | 9 [7] | [7] 11 | [ygeN]–[ygeO] | [ygeN],ygeN,[ygeO] |
* | * | ÷ | CP009273 | 3246068 | 3246223 | 156 | 8 [7] | [7] 8 | yhaH/yhaI | DUF805 family inner membrane protein/DUF805 family inner membrane protein |
* | * | ÷ | CP009273 | 3262242 | 3262386 | 145 | 8 [6] | [7] 8 | yhaC | pentapetide repeats‑related protein |
* | * | ÷ | CP009273 | 3575932 | 3576502 | 571 | 8 [7] | [6] 8 | [yhhZ]–[yrhA] | [yhhZ],[yrhA] |
* | * | ÷ | CP009273 | 3577869 | 3578000 | 132 | 9 [7] | [7] 9 | yrhA/yrhB | pseudogene, interrupted by IS1E/stable heat shock chaperone |
* | * | ÷ | CP009273 | 3761713 | 3761890 | 178 | 8 [6] | [4] 8 | yibG | TPR‑like repeat protein |
* | * | ÷ | CP009273 | 3763029 | 3763270 | 242 | 9 [7] | [5] 11 | [yibV]–yibV | [yibV],yibV |
* | * | ÷ | CP009273 | 3791394 | 3791620 | 227 | 8 [6] | [5] 9 | [waaL]–[waaU] | [waaL],[waaU] |
* | * | ÷ | CP009273 | 3792359 | 3792910 | 552 | 8 [6] | [3] 9 | [waaU]–[waaZ] | [waaU],[waaZ] |
* | * | ÷ | CP009273 | 3797791 | 3798512 | 722 | 8 [6] | [7] 8 | [waaS] | [waaS] |
* | * | ÷ | CP009273 | 4294326 | 4294447 | 122 | 8 [7] | [7] 8 | [yjcS] | [yjcS] |
* | * | ÷ | CP009273 | 4466465 | 4466930 | 466 | 8 [7] | [7] 8 | yjgL | uncharacterized protein |
* | * | ÷ | CP009273 | 4531457 | 4531779 | 323 | 8 [7] | [7] 8 | fimB/fimE | tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA |
* | * | ÷ | CP009273 | 4592938 | 4593143 | 206 | 8 [6] | [7] 8 | yjjP/yjjQ | pseudogene, premature stop codon, putative structural protein/putative transcriptional regulator |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | CP009273 | 360104 = | 31 (0.770) | 36 (0.890) | 24/386 | 0.6 | 53.7% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
? | CP009273 | = 360286 | 31 (0.770) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
* | ? | CP009273 | 1203246 = | 45 (1.110) | 14 (0.380) | 14/354 | 1.3 | 33.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | 1205075 = | 14 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |