mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 468,093 | Δ1 bp | 33.3% | coding (40/339 nt) | glnK → | nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB |
| RA | 982,565 | T→A | 35.8% | intergenic (‑127/+476) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,104,736 | C→T | 47.4% | intergenic (‑339/‑55) | opgC ← / → opgG | osmoregulated periplasmic glucan succinylation membrane protein/osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein |
| RA | 1,111,161 | C→A | 49.7% | R293L (CGT→CTT) | lpxL ← | lauryl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 1,123,224 | A→T | 32.2% | intergenic (+39/‑71) | yceM → / → murJ | putative oxidoreductase/putative peptidoglycan lipid II flippase |
| RA | 1,130,039 | G→A | 43.8% | intergenic (+26/‑146) | flgF → / → flgG | flagellar component of cell‑proximal portion of basal‑body rod/flagellar component of cell‑distal portion of basal‑body rod |
| RA | 1,154,028 | G→A | 36.1% | G235D (GGC→GAC) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,274,207 | A→G | 18.6% | A265A (GCA→GCG) | narK → | nitrate/nitrite transporter |
| RA | 2,083,827 | G→C | 37.1% | R52P (CGC→CCC) | hisG → | ATP phosphoribosyltransferase |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 43.5% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,420,353 | A→G | 40.7% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,394 | G→T | 36.6% | intergenic (‑127/+94) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,440,860 | C→A | 54.6% | P31P (CCG→CCT) | aroC ← | chorismate synthase |
| RA | 2,641,079 | G→A | 17.2% | S1523L (TCG→TTG) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,667,677 | G→A | 41.9% | A124V (GCG→GTG) | yphB ← | mutarotase superfamily protein, YphB family |
| RA | 2,718,735 | G→T | 54.7% | P124Q (CCG→CAG) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,719,426 | T→C | 59.4% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 53.3% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,208,019 | A→G | 27.7% | E538E (GAA→GAG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,348,853 | A→G | 16.0% | K257R (AAA→AGA) | gltB → | glutamate synthase, large subunit |
| RA | 3,960,035 | C→G | 36.7% | R87G (CGC→GGC) | rho → | transcription termination factor |
| RA | 4,115,408 | T→C | 13.3% | E444G (GAA→GGA) | priA ← | Primosome factor n' (replication factor Y) |
| RA | 4,390,235 | T→C | 43.0% | I44T (ATC→ACC) | hfq → | global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication |
| RA | 4,490,439 | G→A | 13.8% | pseudogene (170/258 nt) | yjgX ← | pseudogene fragment |
| RA | 4,599,035 | G→A | 21.1% | A191A (GCG→GCA) | yjjG → | dUMP phosphatase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 45 (2.210) | 37/276 | NT | NA | 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 = | 3 (0.150) | 18 (1.000) | 15/244 | NT | 86.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 3 (0.170) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 2 (0.100) | 17 (0.940) | 15/244 | NT | 87.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 3 (0.170) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1381501 | 16 (0.790) | 3 (0.160) | 3/260 | NT | 14.6% | coding (525/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| ? | CP009273 | = 1381567 | 20 (1.040) | coding (591/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase | |||||
| * | ? | CP009273 | = 1391495 | NA (NA) | 4 (0.200) | 4/276 | NT | 33.3% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | CP009273 | = 1972751 | 8 (0.390) | intergenic (‑297/‑483) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 2269338 = | 12 (0.590) | 9 (0.440) | 9/276 | NT | 42.9% | coding (587/1026 nt) | yejE | microcin C transporter YejABEF, permease subunit; ABC family |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2269346 | 12 (0.590) | 12 (0.590) | 12/276 | NT | 50.0% | coding (595/1026 nt) | yejE | microcin C transporter YejABEF, permease subunit; ABC family |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 3360109 | NA (NA) | 6 (0.290) | 5/276 | NT | 40.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 3370794 = | 9 (0.440) | intergenic (‑15/+380) | sspA/rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 | |||||