mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 126,947 | G→T | R418L (CGT→CTT) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 844,358 | C→T | G375S (GGT→AGT) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 1,413,542 | A→T | Y67N (TAT→AAT) | ydaC ← | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| RA | 1,793,898 | Δ1 bp | coding (212/552 nt) | btuE ← | glutathione peroxidase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,093,040 | G→A | A215T (GCT→ACT) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 3,623,585 | A→G | E63G (GAA→GGA) | yhhH → | putative NTF2 fold immunity protein for polymorphic toxin RhsB |
| RA | 4,116,703 | T→G | K173N (AAA→AAC) | glpK ← | glycerol kinase |
| RA | 4,399,892 | A→C | I214L (ATT→CTT) | miaA → | delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423711–3424563 | 3424563 | 1–853 | 42 [41] | [41] 42 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 8 (0.090) | 61 (0.810) | 48/264 | 0.7 | 88.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.120) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 9 (0.110) | 64 (0.850) | 50/264 | 0.6 | 88.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.120) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 79 (0.960) | 66/288 | 0.2 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 83 (0.980) | 69/296 | 0.2 | 97.7% | intergenic (‑91/‑1) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| ? | NC_000913 | = 1652258 | 2 (0.020) | pseudogene (708/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1651547 | NA (NA) | 90 (1.070) | 73/294 | 0.1 | 97.8% | intergenic (+10/‑4) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related |
| ? | NC_000913 | 1652253 = | 2 (0.020) | pseudogene (703/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2406857 = | 2 (0.020) | 81 (0.960) | 60/294 | 0.4 | 97.6% | intergenic (‑218/‑702) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | = 2997688 | NA (NA) | intergenic (‑90/+2) | insC1/ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant | |||||
| * | ? | NC_000913 | = 2406863 | 3 (0.040) | 78 (0.930) | 62/294 | 0.3 | 96.3% | intergenic (‑224/‑696) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | 2996360 = | NA (NA) | intergenic (‑2/+10) | ygeO/insD1 | pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 3186094 = | NA (NA) | 105 (1.240) | 75/296 | 0.1 | 94.6% | intergenic (+6/‑91) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | NC_000913 | 3485933 = | 6 (0.070) | intergenic (‑117/‑185) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||
| * | ? | NC_000913 | = 3187424 | NA (NA) | 81 (0.960) | 64/296 | 0.3 | 95.3% | intergenic (+11/‑1) | insD1/yqiG | IS2 transposase TnpB/pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | NC_000913 | = 3485937 | 4 (0.050) | intergenic (‑121/‑181) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||