breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 418,960 Δ1 bp 100% coding (1072/1296 nt) phoR → sensory histidine kinase in two‑component regulatory system with PhoB
JC JC 700,597 IS1 (–) +9 bp 100% coding (990‑998/1221 nt) nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA 704,083 C→A 100% A47E (GCG→GAG)  nagE → N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components
RA 1,157,896:1 +A 100% coding (28/1434 nt) ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,464,303 G→A 5.9% W255* (TGG→TGA paaX → transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA 1,726,390 G→T 100% R123L (CGC→CTC)  nemR → transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
RA 1,756,374 G→A 100% G226D (GGC→GAC)  pykF → pyruvate kinase I
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,066,465 T→C 100% K286R (AAG→AGG)  insH1 ← IS5 transposase and trans‑activator
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,304,522 G→T 7.3% intergenic (+129/+586) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,523 G→C 7.3% intergenic (+130/+585) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,537 A→G 8.2% intergenic (+144/+571) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,540 C→T 10.0% intergenic (+147/+568) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,549 C→T 9.3% intergenic (+156/+559) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 3,560,455:1 +G 100% 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 100% [rph][rph] [rph], [rph]
MC JC 3,909,312 Δ774 bp 100% [pstA][pstC] [pstA], [pstC]
RA 3,922,565 A→G 5.6% intergenic (‑125/+492) atpI ← / ← rsmG ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA 3,966,675 C→T 6.3% R87C (CGC→TGC)  rho → transcription termination factor
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,102,342 T→G 5.7% V218G (GTG→GGG)  kdgT → 2‑keto‑3‑deoxy‑D‑gluconate transporter
RA 4,171,648 A→C 100% noncoding (12/120 nt) rrfB → 5S ribosomal RNA of rrnB operon
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
JC 4,189,483 +CCGGC 8.0% coding (4134/4224 nt) rpoC → RNA polymerase, beta prime subunit
RA 4,189,483:2 +C 12.4% coding (4134/4224 nt) rpoC → RNA polymerase, beta prime subunit
RA 4,189,512:1 +C 63.3% coding (4163/4224 nt) rpoC → RNA polymerase, beta prime subunit
RA 4,296,060 C→T 14.4% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→G 18.8% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 24.8% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 21.5% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 12.6% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,304 A→C 8.2% intergenic (+510/+132) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) 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 954508 954855 348 43 [34] [37] 38 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ NC_000913 1211528 1212769 1242 40 [36] [37] 39 [icdC]–[ycgX] [icdC],iraM,[ycgX]
* * ÷ NC_000913 1529876 1530536 661 42 [35] [37] 42 [rhsE]–ydcD [rhsE],ydcD
* * ÷ NC_000913 1640598 1641185 588 39 [33] [37] 38 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
* * ÷ NC_000913 2469008 2469812 805 40 [35] [34] 42 [gtrB]–[gtrS] [gtrB],[gtrS]
* * ÷ NC_000913 3268699 3269664 966 38 [36] [35] 39 [yhaC] [yhaC]
* * ÷ NC_000913 3287046 3287438 393 38 [37] [37] 40 [yraH] [yraH]
* * ÷ NC_000913 4110658 4111559 902 38 [36] [37] 38 [cdh]–tpiA [cdh],tpiA
* * ÷ NC_000913 4476646 4477215 570 38 [34] [36] 40 yjgL SopA‑central‑domain‑like hexapeptide repeat protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =32 (0.320)62 (0.670) 53/478 NT 67.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 29 (0.310)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780531 (0.310)81 (0.880) 52/478 NT 73.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 29 (0.310)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1575208 =77 (0.780)4 (0.040) 4/496 NT 5.1% intergenic (‑6/+39) pqqL/yddB putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor
?NC_000913 1575230 = 73 (0.760)intergenic (‑28/+17) pqqL/yddB putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor
* ? NC_000913 2738913 =NA (NA)4 (0.040) 4/486 NT NA intergenic (+8/+35) pheA/tyrA chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase
?NC_000913 2738941 = NA (NA)intergenic (+36/+7) pheA/tyrA chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase
* ? NC_000913 4171223 =0 (0.000)4 (0.040) 4/504 NT 100% noncoding (2583/2904 nt) rrlB 23S ribosomal RNA of rrnB operon
?NC_000913 4212634 = NA (NA)noncoding (2592/2904 nt) rrlE 23S ribosomal RNA of rrnE operon