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 | seq id | position | mutation | annotation | gene | description |
| RA | BN000925 | 8,770 | 3 bp→CGC | coding (1369‑1371/3006 nt) | tnpA → | Tn1 transposase |
| RA | BN000925 | 9,791 | A→G | D797G (GAC→GGC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 9,802 | G→A | D801N (GAC→AAC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,089 | A→C | A896A (GCA→GCC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,359 | T→A | G986G (GGT→GGA) | tnpA → | Tn1 transposase |
| RA | BN000925 | 12,239 | +A | intergenic (‑601/+1055) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,406 | T→G | intergenic (‑768/+888) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,688 | T→A | intergenic (‑1050/+606) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 14,153 | T→A | L35Q (CTG→CAG) | tetA → | tetracycline exporter protein |
| RA | BN000925 | 15,561 | Δ1 bp | intergenic (+312/+320) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,639 | C→G | intergenic (+390/+242) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,898 | +C | coding (649/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 16,410 | +T | coding (137/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 31,028 | C→G | P35A (CCC→GCC) | trbP → | TrbP protein |
| RA | BN000925 | 31,939 | 3 bp→GCG | coding (263‑265/420 nt) | upf31.7 → | hypothetical protein |
| RA | BN000925 | 36,655 | A→G | R116G (AGA→GGA) R108G (AGA→GGA) |
istA → istA → |
IS21 transposase IS21 transposase |
| RA | BN000925 | 38,388 | A→C | pseudogene (45/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,390 | 1 bp→AG | pseudogene (47/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,393 | C→T | pseudogene (50/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,421 | Δ1 bp | pseudogene (78/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,510 | Δ1 bp | pseudogene (167/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,526 | Δ1 bp | intergenic (+12/‑232) | upf35.8 → / → aphA | probable truncation of theoretical product due to sequence errors/aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,136 | Δ1 bp | coding (379/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,147 | Δ1 bp | coding (390/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,179 | +CG | coding (422/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 53,069 | +T | intergenic (+42/+10) | traM → / ← kfrC | TraM protein/KfrC protein |
| RA | BN000925 | 54,833 | Δ1 bp | intergenic (‑32/+127) | kfrB ← / ← kfrA | KfrB protein/KfrA coiled‑coil protein |
| RA | BN000925 | 56,817 | Δ1 bp | coding (297/522 nt) | korF ← | KorF repressor protein |
| MC JC | NC_000913 | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | NC_000913 | 793,915 | Δ55 bp | coding (676‑730/789 nt) | modE ← | DNA‑binding transcriptional dual regulator ModE |
| JC JC | NC_000913 | 986,763 | IS1 (+) +9 bp | coding (212‑220/1089 nt) | ompF ← | outer membrane porin F |
| JC JC | NC_000913 | 1,258,932 | IS5 (+) +4 bp | coding (142‑145/279 nt) | ychH → | stress‑induced protein |
| MC JC | NC_000913 | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| JC JC | NC_000913 | 1,978,195 | IS1 (–) +9 bp | [flhD] | [flhD] | |
| RA | NC_000913 | 1,991,819 | A→C | noncoding (83/87 nt) | leuZ ← | tRNA‑Leu |
| RA | NC_000913 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | NC_000913 | 2,249,587 | A→T | F11Y (TTT→TAT) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | NC_000913 | 3,027,491 | G→T | G124V (GGC→GTC) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| MC JC | NC_000913 | 3,366,751 | Δ295 bp | IS5‑mediated | yhcE–[yhcF] | yhcE, [yhcF] |
| RA | NC_000913 | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | NC_000913 | 3,717,751 | C→T | L148L (CTG→TTG) | ghrB → | glyoxylate reductase |
| RA | NC_000913 | 4,212,959 | G→C | intergenic (+13/‑81) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,212,973 | Δ1 bp | intergenic (+27/‑67) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423758–3424234 | 3424535–3424238 | 5–778 | 52 [51] | [50] 52 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 30 (0.270) | 92 (0.900) | 55/376 | 0.8 | 76.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 28 (0.270) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 30 (0.270) | 84 (0.820) | 58/376 | 0.6 | 75.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 28 (0.270) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||