breseq  version 0.27.1  revision 87c22d663cc3
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 668,742 C→G E99Q (GAA→CAA)  rsfS ← ribosomal silencing factor
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,245 T→C L375L (TTA→CTA)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,196,247 A→G L375L (TTA→TTG)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
RA 1,677,707 G→T S66* (TCA→TAA)  pntA ← pyridine nucleotide transhydrogenase, alpha subunit
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 2,513,351 C→A L104M (CTG→ATG)  nupC → nucleoside (except guanosine) transporter
JC JC 2,536,312 Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp coding (479‑484/510 nt) crr → glucose‑specific enzyme IIA component of PTS
JC 2,866,957 (TTGCTCTGC)1→2 coding (595/993 nt) rpoS ← RNA polymerase, sigma S (sigma 38) factor
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
RA 3,815,810 Δ1 bp intergenic (‑42/+24) pyrE ← / ← rph orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
RA 4,160,854 C→T intergenic (‑64/‑270) sthA ← / → fabR pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB
MC JC 4,233,804 1557 bp→83 bp coding (47‑1603/1650 nt) pgi → glucosephosphate isomerase
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 582749 584688 1940 41 [40] [40] 42 [ybcY]–[ompT] [ybcY], ybcY, tfaX, appY, [ompT]
* * ÷ NC_000913 720820 721216 397 43 [38] [40] 42 [ybfK]–[kdpE] [ybfK], [kdpE]
* * ÷ NC_000913 1196264 1212862 16599 41 [40] [38] 42 [icd]–[ycgX] 27 genes
[icd], ymfD, ymfE, lit, intE, xisE, ymfI, ymfJ, cohE, croE, ymfL, ymfM, oweE, aaaE, ymfR, beeE, jayE, ymfQ, stfP, tfaP, tfaE, stfE, pinE, mcrA, icdC, iraM, [ycgX]
* * ÷ NC_000913 1529886 1530670 785 41 [40] [40] 42 [rhsE]–[yncI] [rhsE], ydcD, [yncI]
* * ÷ NC_000913 1812500 1813372 873 41 [38] [40] 42 [ydjO] [ydjO]
* * ÷ NC_000913 1978319 1979730 1412 41 [40] [40] 41 insB1–insA insB1, insA
* * ÷ NC_000913 2033460 2034119 660 42 [36] [38] 43 [yedR]–[yedS] [yedR], [yedS]
* * ÷ NC_000913 2103235 2104225 991 41 [37] [40] 42 [wbbL]–[wbbK] [wbbL], [wbbK]
* * ÷ NC_000913 2455567 2456224 658 41 [40] [39] 42 [yfcV] [yfcV]
* * ÷ NC_000913 2469019 2470744 1726 42 [39] [40] 42 [gtrB]–gtrS [gtrB], gtrS
* * ÷ NC_000913 2990595 2991375 781 41 [39] [40] 42 [ygeF]–[ygeG] [ygeF], ygeF, [ygeG]
* * ÷ NC_000913 2994992 2995973 982 42 [40] [40] 42 [ygeK]–[ygeO] [ygeK], ygeN, [ygeN], [ygeO]
* * ÷ NC_000913 3287001 3287450 450 42 [40] [40] 42 [agaI]–[yraH] [agaI], [yraH]
* * ÷ NC_000913 3653461 3653955 495 43 [39] [40] 41 [yhiS] [yhiS]
* * ÷ NC_000913 3769467 3770249 783 41 [38] [40] 41 [yibV]–[yibH] [yibV], yibV, yibU, yibU, [yibH]
* * ÷ NC_000913 3796911 3800325 3415 42 [38] [40] 42 [waaC]–[waaY] [waaC], waaL, waaU, waaZ, [waaY]
* * ÷ NC_000913 3804164 3805192 1029 42 [39] [39] 43 waaS–[waaP] waaS, [waaP]
* * ÷ NC_000913 4282138 4283261 1124 43 [38] [40] 41 [yjcF]–[actP] [yjcF], [actP]
* * ÷ NC_000913 4476465 4477229 765 41 [39] [37] 46 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4541560 4542086 527 43 [38] [39] 41 [fimE] [fimE]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 12994980 (0.000)32 (0.310) 30/570 2.1 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein