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 | annotation | gene | description |
| RA | 280,246 | T→G | A445A (GCT→GCG) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 309,254 | G→A | intergenic (‑301/+173) | ykgR ← / ← ykgP | uncharacterized protein/pseudogene, oxidoreductase family |
| RA | 1,613,656 | C→T | R94C (CGC→TGC) | marR → | transcriptional repressor of multiple antibiotic resistance |
| JC JC | 1,765,315 | IS5 (+) +4 bp | intergenic (+87/‑10) | ydiL → / → ydiM | putative HTH domain DNA‑binding protein/MFS superfamily sugar transport 1 family protein |
| RA | 2,802,100 | T→C | pseudogene (426/1178 nt) | ygaY → | pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein |
| RA | 3,959,963 | G→T | G63C (GGT→TGT) | rho → | transcription termination factor |
| RA | 4,214,915 | C→T | A387V (GCG→GTG) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,493,435 | (T)6→7 | intergenic (‑187/‑440) | insG ← / → yjhB | IS4 transposase/putative transporter |
| JC JC | 4,630,235 | IS30 (+) +2 bp | coding (17‑18/141 nt) | yjjY → | uncharacterized protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 946667 | 949084 | 2418 | 224 [221] | [221] 223 | pflB–[focA] | pflB,[focA] |
| * | * | ÷ | CP009273 | 1290816 | 1293662 | 2847 | 227 [219] | [222] 226 | adhE | adhE |
| * | * | ÷ | CP009273 | 1392958 | 1437161 | 44204 | 224 [218] | [220] 224 | fnr–ldhA | fnr,ogt,abgT,abgB,abgA,abgR,mcaS,smrA,ydaM,ydaN,fnrS,dbpA,ttcA,intR,ydaQ,rcbA,ralR,recT,recE,racC,ydaE,kilR,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,ydaW,rzpR,rzoR,trkG,ynaK,ydaY,tmpR,lomR,insH1,lomR,stfR,tfaR,pinR,ynaE,ttcC,uspF,ompN,micC,pfo,ydbJ,hslJ,ldhA |
| * | * | ÷ | CP009273 | 2408142 | 2410437 | 2296 | 224 [217] | [222] 226 | [ackA]–pta | [ackA],pta |
| * | * | ÷ | CP009273 | 4369109 | 4370414 | 1306 | 224 [222] | [221] 225 | [frdD]–[frdA] | [frdD],frdC,frdB,[frdA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 388 (0.970) | 310 (0.770) | 167/300 | 1.0 | 44.4% | 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 = | 44 (0.110) | 288 (0.800) | 160/268 | 0.5 | 84.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 69 (0.190) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 45 (0.110) | 315 (0.880) | 157/268 | 0.6 | 85.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 69 (0.190) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1391495 | NA (NA) | 387 (0.970) | 190/300 | 0.3 | 96.3% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | CP009273 | = 1972751 | 15 (0.040) | intergenic (‑297/‑483) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1972748 = | 21 (0.050) | 396 (0.990) | 168/298 | 0.9 | 95.0% | intergenic (‑294/‑486) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 2283592 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||