breseq  version 0.26.1  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
MC JC 257,908 Δ776 bp [crl] [crl]
RA 691,331 C→A D152Y (GAC→TAC)  ybeX ← putative ion transport
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,567,761 T→C D116G (GAC→GGC)  eutH ← ethanolamine transporter
RA 3,440,087 C→T G315S (GGC→AGC)  rpoA ← RNA polymerase, alpha subunit
RA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
MC JC 3,815,859 Δ82 bp [rph]–[rph] [rph], [rph]
RA 3,966,676 G→T R87L (CGC→CTC)  rho → transcription termination factor
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 522843 523217 375 33 [24] [30] 31 ybbP/rhsD putative ABC transporter permease/Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
* * ÷ NC_000913 527205 528067 863 32 [27] [30] 31 [rhsD]–[rhsH] [rhsD], ybbC, [rhsH]
* * ÷ NC_000913 528572 528938 367 34 [30] [30] 31 [rhsH]–[ybbD] [rhsH], [ybbD]
* * ÷ NC_000913 568625 568869 245 31 [29] [25] 32 [emrE] [emrE]
* * ÷ NC_000913 576796 577131 336 31 [28] [29] 31 [nmpC] [nmpC]
* * ÷ NC_000913 583007 583876 870 31 [28] [26] 31 [tfaX]–[appY] [tfaX], [appY]
* * ÷ NC_000913 584001 584236 236 31 [29] [24] 32 appY global transcriptional activator; DLP12 prophage
* * ÷ NC_000913 637610 637880 271 31 [29] [30] 31 [ybdO]–[dsbG] [ybdO], [dsbG]
* * ÷ NC_000913 1050696 1050899 204 32 [29] [24] 34 insB1/cspH IS1 transposase B/stress protein, member of the CspA‑family
* * ÷ NC_000913 1197514 1197853 340 31 [28] [24] 32 [ymfD]–[ymfE] [ymfD], [ymfE]
* * ÷ NC_000913 1299347 1300726 1380 31 [22] [26] 32 ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* * ÷ NC_000913 1526748 1527718 971 31 [28] [30] 31 [yncG]–yncH [yncG], yncH
* * ÷ NC_000913 1640620 1640782 163 35 [28] [30] 32 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
* * ÷ NC_000913 1978393 1979315 923 31 [30] [27] 36 insB1–insA insB1, insA
* * ÷ NC_000913 1979490 1979656 167 67 [0] [30] 31 insA/uspC IS1 repressor TnpA/universal stress protein
* * ÷ NC_000913 2033542 2034123 582 31 [28] [27] 33 [yedS] [yedS]
* * ÷ NC_000913 2106561 2106991 431 36 [30] [23] 31 wbbH O‑antigen polymerase
* * ÷ NC_000913 2137602 2137808 207 31 [29] [30] 43 wza/yegH colanic acid export protein; outer membrane auxillary lipoprotein/inner membrane protein
* * ÷ NC_000913 2150915 2151192 278 31 [30] [28] 31 [yegI]–[yegJ] [yegI], [yegJ]
* * ÷ NC_000913 2192196 2192526 331 33 [29] [30] 37 [yehD]–[yehE] [yehD], [yehE]
* * ÷ NC_000913 2344225 2344625 401 31 [30] [29] 31 yfaL/nrdA adhesin/ribonucleoside‑diphosphate reductase 1, alpha subunit
* * ÷ NC_000913 2469118 2469861 744 32 [29] [30] 32 [gtrB]–[gtrS] [gtrB], [gtrS]
* * ÷ NC_000913 2629388 2629817 430 31 [30] [30] 31 [yfgG]–[yfgH] [yfgG], [yfgH]
* * ÷ NC_000913 2773307 2774041 735 31 [22] [26] 32 [yfjW] [yfjW]
* * ÷ NC_000913 2774335 2775164 830 32 [27] [30] 31 [yfjW] [yfjW]
* * ÷ NC_000913 2784404 2785380 977 32 [30] [30] 32 [ypjC] [ypjC]
* * ÷ NC_000913 2785775 2786665 891 31 [30] [27] 31 [ileY]–[ygaQ] [ileY], [ygaQ]
* * ÷ NC_000913 2903536 2903937 402 33 [30] [28] 32 ygcE/queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
* * ÷ NC_000913 2989288 2989623 336 31 [29] [27] 31 [yqeI]–[yqeJ] [yqeI], [yqeJ]
* * ÷ NC_000913 3268634 3269435 802 31 [29] [29] 32 yhaC pentapetide repeats‑related protein
* * ÷ NC_000913 3360835 3361169 335 41 [30] [16] 32 gltD/gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
* * ÷ NC_000913 3423759–3424234 3424562–3424238 5–804 31 [30] [30] 31 [rrfD]–[rrlD] [rrfD], [rrlD]
* * ÷ NC_000913 3769467 3770226 760 32 [25] [29] 31 [yibV]–yibU [yibV], yibV, yibU, yibU
* * ÷ NC_000913 3804154 3804540 387 31 [28] [29] 31 [waaS] [waaS]
* * ÷ NC_000913 3804652 3805176 525 31 [28] [27] 31 [waaS]–[waaP] [waaS], [waaP]
* * ÷ NC_000913 4251385 4251993 609 33 [30] [25] 31 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ NC_000913 4475979 4476080 102 32 [30] [28] 32 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4476781 4477156 376 31 [29] [28] 39 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4542550 4542924 375 35 [30] [23] 31 [fimE] [fimE]

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =4 (0.050)99 (1.380) 56/266 0.1 93.6% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 10 (0.140)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078053 (0.040)49 (0.680) 39/266 0.7 88.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 10 (0.140)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 19794890 (0.000)67 (0.830) 40/298 0.9 100% intergenic (‑274/‑264) insA/uspC IS1 repressor TnpA/universal stress protein
?NC_000913 = 2290113 NA (NA)noncoding (1/1195 nt) IS5 repeat region