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 2,019,460 G→A V359I (GTC→ATC)  fliK → flagellar hook‑length control protein
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 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
JC JC 3,890,075 IS5 (–) +4 bp coding (1346‑1349/1416 nt) tnaA → tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
RA 3,966,667 G→T S84I (AGC→ATC)  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 582740 583916 1177 33 [30] [32] 34 [ybcY]–[appY] [ybcY], ybcY, tfaX, [appY]
* * ÷ NC_000913 954543 954834 292 33 [32] [32] 33 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ NC_000913 1212020 1212819 800 33 [26] [28] 33 [ycgX] [ycgX]
* * ÷ NC_000913 1529943 1530540 598 33 [32] [31] 33 [ydcD] [ydcD]
* * ÷ NC_000913 1640610 1640805 196 33 [32] [32] 34 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
* * ÷ NC_000913 1812614 1813370 757 34 [32] [32] 33 [ydjO] [ydjO]
* * ÷ NC_000913 2033522 2034076 555 33 [32] [32] 34 [yedS] [yedS]
* * ÷ NC_000913 2469055 2469906 852 35 [29] [32] 34 [gtrB]–[gtrS] [gtrB], [gtrS]
* * ÷ NC_000913 2773307 2774059 753 36 [23] [31] 35 [yfjW] [yfjW]
* * ÷ NC_000913 2774317 2775260 944 33 [32] [31] 33 [yfjW] [yfjW]
* * ÷ NC_000913 2784320 2785534 1215 33 [27] [32] 36 [ypjC] [ypjC]
* * ÷ NC_000913 2825625 2825829 205 34 [31] [31] 33 mltB/srlA membrane‑bound lytic murein transglycosylase B/glucitol/sorbitol‑specific enzyme IIC component of PTS
* * ÷ NC_000913 2990628 2991347 720 33 [31] [31] 33 [ygeF]–[ygeG] [ygeF], ygeF, [ygeG]
* * ÷ NC_000913 2994872 2995520 649 35 [31] [31] 33 [ygeK]–[ygeN] [ygeK], [ygeN]
* * ÷ NC_000913 3268599 3269736 1138 33 [30] [32] 35 [yhaC] [yhaC]
* * ÷ NC_000913 3360722 3361207 486 33 [32] [31] 33 [gltF] [gltF]
* * ÷ NC_000913 3423760–3424235 3424549–3424238 4–790 33 [30] [32] 33 [rrfD]–[rrlD] [rrfD], [rrlD]
* * ÷ NC_000913 3455293 3455732 440 33 [32] [32] 33 [gspA]–[gspC] [gspA], [gspC]
* * ÷ NC_000913 3769467 3770045 579 37 [32] [32] 35 [yibV]–[yibU] [yibV], yibV, yibU, [yibU]
* * ÷ NC_000913 3798867 3799544 678 40 [24] [31] 35 [waaU]–[waaZ] [waaU], [waaZ]
* * ÷ NC_000913 3804156 3805180 1025 35 [27] [29] 36 waaS–[waaP] waaS, [waaP]
* * ÷ NC_000913 4086825 4087046 222 33 [31] [32] 33 [fdhD]–[yiiG] [fdhD], [yiiG]
* * ÷ NC_000913 4251394 4252029 636 33 [32] [28] 34 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 24629338 (0.100)162 (2.010) 77/310 0.0 95.3% intergenic (+287/‑79) fadL/yfdF long‑chain fatty acid outer membrane transporter/uncharacterized protein
?NC_000913 = 3131340 NA (NA)noncoding (1195/1195 nt) IS5 repeat region