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 84,962 G→A 9.1% A150T (GCC→ACC)  cra → transcriptional repressor‑activator for carbon metabolism
RA 227,132 C→A 20.9% A79A (GCG→GCT yafC ← LysR family putative transcriptional regulator
JC 481,304 +CATCCAC 100% coding (88/648 nt) acrR → transcriptional repressor
RA 663,136 A→G 8.0% S180P (TCG→CCG)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 982,290 Δ1 bp 100% coding (149/1089 nt) ompF ← outer membrane porin 1a (Ia;b;F)
RA 1,428,899 G→A 100% intergenic (‑418/+316) ynaE ← / ← ttcC cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA 1,602,426 Δ1 bp 22.7% coding (854/915 nt) yneE ← bestrophin family putative inner membrane protein
RA 1,602,427 Δ1 bp 23.3% coding (853/915 nt) yneE ← bestrophin family putative inner membrane protein
RA 1,607,154 C→T 12.4% G119S (GGT→AGT)  glsB ← glutaminase 2
RA 1,616,797 G→T 12.6% intergenic (+21/‑106) ydeE → / → yneM putative transporter/inner membrane‑associated protein
RA 1,737,690 Δ1 bp 30.6% intergenic (‑191/‑24) ribC ← / → mdtK riboflavin synthase, alpha subunit/multidrug efflux system transporter
JC 2,305,823 +GGTGTC 24.4% coding (406/1104 nt) ompC ← outer membrane porin protein C
RA 2,332,659 C→A 100% G81C (GGT→TGT)  gyrA ← DNA gyrase (type II topoisomerase), subunit A
RA 2,333,563 G→A 10.0% G173D (GGT→GAT)  ubiG → bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase
RA 2,913,718 G→T 7.2% P130T (CCG→ACG)  gudX ← glucarate dehydratase‑related protein, substrate unknown
RA 3,010,197:1 +G 100% coding (779/3099 nt) ygfK → putative Fe‑S subunit oxidoreductase subunit
RA 3,167,383 G→A 100% S458L (TCG→TTG)  parE ← DNA topoisomerase IV, subunit B
JC 3,208,014 +CCGAAAGCCTGCGTG 48.7% coding (1609/1842 nt) rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 3,638,574 G→A 5.9% intergenic (‑32/‑171) prlC ← / → rlmJ oligopeptidase A/23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA 3,678,601 C→A 7.6% S126S (TCG→TCT yhjK ← cyclic‑di‑GMP phosphodiesterase
RA 3,872,086 T→C 100% Q465R (CAG→CGG)  gyrB ← DNA gyrase, subunit B
RA 3,872,761 A→G 7.4% I240T (ATC→ACC)  gyrB ← DNA gyrase, subunit B
RA 3,877,753 G→A 6.7% A20T (GCT→ACT)  rpmH → 50S ribosomal subunit protein L34
RA 4,234,832 C→T 8.0% A58T (GCC→ACC)  malF ← maltose transporter subunit
RA 4,267,384 Δ1 bp 100% intergenic (‑73/‑13) soxS ← / → soxR superoxide response regulon transcriptional activator; autoregulator/redox‑sensitive transcriptional activator of soxS; autorepressor
RA 4,441,503 A→G 7.1% Q210R (CAG→CGG)  ytfR → putative ABC superfamily sugar transporter ATP‑binding subunit

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 380411 380485 75 7 [4] [3] 6 yaiS/tauA putative PIG‑L family deacetylase/taurine transporter subunit
* * ÷ CP009273 579513 579587 75 8 [5] [5] 6 appY global transcriptional activator; DLP12 prophage
* * ÷ CP009273 716364 716527 164 8 [5] [4] 9 [kdpE] [kdpE]
* * ÷ CP009273 731799 731880–731868 70–82 6 [5] [5] 6 ybfC/ybfQ putative periplasmic protein/pseudogene, H repeat‑associated protein
* * ÷ CP009273 766290 766346 57 6 [5] [3] 6 mngB/cydA alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
* * ÷ CP009273 950048 950253 206 8 [5] [5] 6 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ CP009273 993036 993260 225 6 [5] [4] 6 ssuE/elfA NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit
* * ÷ CP009273 1193141 1193258 118 6 [5] [3] 9 ymfE e14 prophage; putative inner membrane protein
* * ÷ CP009273 1193847 1193935–1193911 65–89 6 [5] [5] 6 ymfE/lit e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
* * ÷ CP009273 1207125 1207167 43 6 [4] [4] 6 [iraM] [iraM]
* * ÷ CP009273 1207523 1207602 80 6 [3] [5] 6 iraM/ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
* * ÷ CP009273 1225848 1226006 159 6 [3] [5] 6 [hlyE] [hlyE]
* * ÷ CP009273 1540206 1540501 296 7 [5] [5] 6 [yddL] [yddL]
* * ÷ CP009273 1592506 1592612 107 6 [5] [5] 6 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ CP009273 1634945 1635033 89 6 [4] [3] 6 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
* * ÷ CP009273 1980120 1980230 111 6 [5] [5] 6 araF/ftnB L‑arabinose transporter subunit/ferritin B, putative ferrous iron reservoir
* * ÷ CP009273 2185796 2185959 164 8 [4] [5] 6 yehD/yehE putative fimbrial‑like adhesin protein/DUF2574 family protein
* * ÷ CP009273 2456685 2456723 39 6 [5] [5] 6 yfdF uncharacterized protein
* * ÷ CP009273 2462618 2462687 70 7 [5] [4] 6 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2898912 2899059 148 6 [5] [5] 6 yqcG yqcG
* * ÷ CP009273 3576412 3576499 88 6 [5] [5] 6 yrhA pseudogene, interrupted by IS1E
* * ÷ CP009273 4258831 4258865 35 6 [4] [3] 6 yjbS uncharacterized protein
* * ÷ CP009273 4561727 4561819 93 6 [5] [5] 7 [yjiS] [yjiS]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =32 (0.910)37 (1.050) 30/274 NT 52.9% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 34 (0.960)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 1203246 =0 (0.000)28 (0.900) 26/242 NT 100% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 0 (0.000)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 12032610 (0.000)25 (0.800) 20/242 NT 100% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 0 (0.000)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 160333620 (0.570)8 (0.230) 8/274 NT 33.3% intergenic (‑57/+150) yneE/uxaB bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
?CP009273 1605114 = 12 (0.340)intergenic (‑177/+50) uxaB/yneF altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
* ? CP009273 1721915 =30 (0.850)49 (1.390) 35/274 NT 59.8% coding (1000/1098 nt) nemA chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme
?CP009273 = 1740277 36 (1.020)coding (108/1257 nt) ydhQ autotransporter adhesin‑related protein