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 | freq | annotation | gene | description |
| RA | 14,485:1 | +G | 71.8% | coding (318/1131 nt) | dnaJ → | chaperone Hsp40, DnaK co‑chaperone |
| RA | 171,746 | T→C | 12.1% | V51V (GTT→GTC) | clcA → | H(+)/Cl(‑) exchange transporter |
| MC JC | 248,669 | Δ14 bp | 100% | coding (178‑191/294 nt) | yafN → | antitoxin of the YafO‑YafN toxin‑antitoxin system |
| RA | 284,666 | C→A | 11.5% | E70* (GAG→TAG) | yagI ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 292,852 | G→T | 100% | intergenic (‑45/‑65) | intF ← / → ptwF | CP4‑6 prophage; putative phage integrase/tRNA‑OTHER |
| RA | 481,171 | Δ1 bp | 100% | intergenic (‑96/‑46) | acrA ← / → acrR | multidrug efflux system/transcriptional repressor |
| RA | 960,678 | G→T | 100% | W301C (TGG→TGT) | ycaI → | ComEC family inner membrane protein |
| RA | 981,654 | Δ2 bp | 100% | coding (784‑785/1089 nt) | ompF ← | outer membrane porin 1a (Ia;b;F) |
| RA | 1,336,256 | G→T | 15.5% | D27Y (GAT→TAT) | pyrF → | orotidine‑5'‑phosphate decarboxylase |
| RA | 1,379,108 | G→A | 20.0% | A245A (GCG→GCA) | ycjX → | DUF463 family protein, putative P‑loop NTPase |
| RA | 1,466,527 | G→T | 8.9% | pseudogene (1754/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 2,008,466 | A→G | 7.5% | T36A (ACC→GCC) | fliG → | flagellar motor switching and energizing component |
| RA | 2,104,588 | G→T | 11.1% | L290L (CTC→CTA) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase subunit, NAD(P)‑binding, of dTDP‑L‑rhamnose synthase |
| RA | 2,314,158 | C→A | 9.4% | R213S (CGC→AGC) | atoS → | sensory histidine kinase in two‑component regulatory system with AtoC |
| JC | 2,332,650 | (CCG)2→1 | 90.1% | coding (248‑250/2628 nt) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,848,801 | G→T | 9.8% | E369* (GAG→TAG) | fhlA → | formate hydrogenlyase transcriptional activator |
| RA | 2,885,943 | A→G | 9.7% | intergenic (+5/‑73) | queD → / → ygcN | 6‑pyruvoyl tetrahydrobiopterin synthase (PTPS)/putative oxidoreductase |
| RA | 3,167,384 | A→G | 100% | S458P (TCG→CCG) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,213,182 | A→G | 10.7% | Q110Q (CAA→CAG) | patA → | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent |
| RA | 3,360,812 | C→A | 8.2% | L176L (CTC→CTA) | yhcF → | putative transcriptional regulator |
| RA | 3,529,153 | G→T | 8.5% | A25A (GCC→GCA) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,591,646 | C→T | 100% | G101G (GGC→GGT) | panM → | PanD autocleavage accelerator, panothenate synthesis |
| RA | 3,639,713 | T→G | 100% | S19A (TCC→GCC) | gor → | glutathione oxidoreductase |
| RA | 3,695,494 | C→A | 10.2% | T245T (ACG→ACT) | dppF ← | dipeptide transporter |
| RA | 3,872,089 | G→T | 91.9% | S464Y (TCT→TAT) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,904,085 | G→T | 7.6% | T267T (ACC→ACA) | pstS ← | periplasmic phosphate binding protein, high‑affinity |
| RA | 4,190,004 | T→C | 7.1% | G191G (GGT→GGC) | yjaG → | DUF416 domain protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1524575 | 1524615 | 41 | 6 [5] | [5] 6 | ydcD | uncharacterized protein |
| * | * | ÷ | CP009273 | 1631811 | 1631896 | 86 | 6 [5] | [5] 6 | [gnsB] | [gnsB] |
| * | * | ÷ | CP009273 | 1631930 | 1631998 | 69 | 6 [5] | [3] 6 | gnsB | Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts) |
| * | * | ÷ | CP009273 | 2050154 | 2050223 | 70 | 6 [5] | [5] 6 | amn/yeeN | AMP nucleosidase/UPF0082 family protein |
| * | * | ÷ | CP009273 | 2779847 | 2779917 | 71 | 6 [5] | [5] 6 | ygaQ | uncharacterized protein; putative enzyme |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 25 (0.650) | 67 (1.730) | 45/276 | NT | 69.1% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | 35 (0.900) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||