breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 124,241 C→T 100% Q409* (CAG→TAG)  aceE → pyruvate dehydrogenase E1 component
MC JC 257,908 Δ776 bp 100% insB9–[crl] insB9, insA9, [crl]
RA 461,007 T→G 100% I707S (ATC→AGC)  lon → Lon protease
RA 569,160 G→T 5.6% D87Y (GAC→TAC)  ybcK → DLP12 prophage; putative recombinase
RA 696,470 C→T 100% noncoding (35/75 nt) glnX ← tRNA‑Gln
RA 754,446 A→G 100% L8P (CTC→CCC)  gltA ← citrate synthase
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
MC JC 1,299,499 Δ1,199 bp 100% insH21 insH21
MC JC 1,978,503 Δ776 bp 100% insB‑5–insA‑5 insB‑5, insA‑5
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA‑5 ← / → uspC IS1 protein InsA/universal stress protein C
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative colanic acid biosynthesis glycosyl transferase
RA 2,173,361 Δ2 bp 100% pseudogene (917‑918/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,661,821 C→G 100% C104S (TGC→TCC)  iscR ← DNA‑binding transcriptional dual regulator IscR
RA 3,041,634 A→C 100% T108P (ACC→CCC)  ygfZ → folate‑binding protein
RA 3,473,614 C→T 100% W156* (TGG→TGA)  rpsG ← 30S ribosomal subunit protein S7
RA 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,780,846 C→T 39.9% G340G (GGC→GGT)  lldD → L‑lactate dehydrogenase
MC JC 3,815,859 Δ82 bp 100% [rph] [rph]
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 5210 5250 41 2 [1] [1] 2 [yaaX] [yaaX]
* * ÷ NC_000913 7523 7676 154 2 [1] [1] 2 yaaJ putative transporter YaaJ
* * ÷ NC_000913 222776 222802 27 2 [1] [1] 2 metN/gmhB L‑methionine/D‑methionine ABC transporter ATP binding subunit/D‑glycero‑beta‑D‑manno‑heptose‑1,7‑bisphosphate 7‑phosphatase
* * ÷ NC_000913 353210 353341 132 2 [1] [1] 2 prpE propionyl‑CoA synthetase
* * ÷ NC_000913 365868 366012 145 2 [0] [1] 2 lacZ beta‑galactosidase
* * ÷ NC_000913 366271 366339 69 3 [1] [1] 2 [lacZ] [lacZ]
* * ÷ NC_000913 536785 536818 34 2 [1] [1] 2 glxR tartronate semialdehyde reductase 2
* * ÷ NC_000913 678414 678447 34 2 [1] [1] 3 djlB putative chaperone
* * ÷ NC_000913 1209603 1209618 16 11 [0] [0] 9 stfE e14 prophage; putative side tail fiber protein fragment
* * ÷ NC_000913 1432079 1432123 45 2 [1] [1] 2 stfR Rac prophage; putative membrane protein
* * ÷ NC_000913 1672911 1672936 26 2 [1] [1] 2 mdtI multidrug/spermidine efflux pump membrane subunit MdtI
* * ÷ NC_000913 1678601 1678649 49 2 [1] [1] 2 ydgH DUF1471 domain‑containing protein YdgH
* * ÷ NC_000913 1697569 1697612 44 2 [1] [1] 2 hdhA 7‑alpha‑hydroxysteroid dehydrogenase
* * ÷ NC_000913 1763836 1763863 28 3 [1] [1] 2 sufB Fe‑S cluster scaffold complex subunit SufB
* * ÷ NC_000913 1930931 1931013 83 2 [1] [1] 2 purT phosphoribosylglycinamide formyltransferase 2
* * ÷ NC_000913 1955094 1955142 49 2 [1] [1] 2 torZ trimethylamine N‑oxide reductase 2
* * ÷ NC_000913 2066232–2066595 2066595 1–364 2 [1] [1] 3 [insH‑6] [insH‑6]
* * ÷ NC_000913 2130897 2130997 101 2 [1] [1] 2 wcaC putative colanic acid biosynthesis glycosyl transferase
* * ÷ NC_000913 2146018 2146057 40 2 [1] [1] 2 dgcE putative diguanylate cyclase DgcE
* * ÷ NC_000913 2457193 2457248 56 2 [1] [1] 2 fadJ 3‑hydroxyacyl‑CoA dehydrogenase FadJ
* * ÷ NC_000913 2879929 2879949 21 2 [1] [1] 2 casE pre‑CRISPR RNA endonuclease
* * ÷ NC_000913 3423798–3424224 3424518–3424238 15–721 2 [1] [1] 2 [rrlD] [rrlD]
* * ÷ NC_000913 3705140 3705222 83 2 [1] [1] 2 dppB dipeptide ABC transporter membrane subunit DppB
* * ÷ NC_000913 3897126 3897258 133 2 [1] [1] 2 yieH 6‑phosphogluconate phosphatase
* * ÷ NC_000913 4145107 4145129 23 2 [1] [1] 2 pflD putative formate acetyltransferase 2

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 556631 =5 (0.490)3 (0.310) 3/246 NT 38.3% intergenic (‑78/+30) ybcI/ybcJ conserved inner membrane protein YbcI/putative RNA‑binding protein YbcJ
?NC_000913 556653 = 5 (0.520)intergenic (‑100/+8) ybcI/ybcJ conserved inner membrane protein YbcI/putative RNA‑binding protein YbcJ
* ? NC_000913 566777 =NA (NA)494 (48.560) 185/262 NT 98.0% noncoding (1/1258 nt) IS3 repeat region
?NC_000913 = 572471 10 (0.980)coding (6/456 nt) ybcN DLP12 prophage; DNA base‑flipping protein
* ? NC_000913 1207790 =0 (0.000)6 (0.670) 5/232 NT 100% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 0 (0.000)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12078051 (0.100)8 (0.890) 8/232 NT 94.8% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 0 (0.000)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 2520948 =7 (0.680)3 (0.300) 3/254 NT 35.9% noncoding (18/76 nt) valU tRNA‑Val
?NC_000913 2521083 = 4 (0.410)noncoding (33/76 nt) valX tRNA‑Val