breseq  version 0.35.4  revision f352f80f4bc9
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 1,935,005 A→C V437G (GTA→GGA)  zwf ← glucose‑6‑phosphate 1‑dehydrogenase
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
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 2,317,667 T→G E737A (GAA→GCA)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,632,046 G→T P164T (CCG→ACG)  guaA ← GMP synthetase (glutamine aminotransferase)
RA 3,002,530 G→A G729D (GGT→GAT)  xdhA → xanthine dehydrogenase, molybdenum binding subunit
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 4,186,577 G→C D410H (GAT→CAT)  rpoC → RNA polymerase, beta prime subunit
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 3423801–3424234 3424542–3424238 5–742 4 [3] [2] 4 [rrlD] [rrlD]
* * ÷ NC_000913 3514394 3515058 665 4 [3] [3] 5 rpe D‑ribulose‑5‑phosphate 3‑epimerase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 225078 =NA (NA)5 (0.150) 5/226 2.6 NA noncoding (1308/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
?NC_000913 225100 = NA (NA)noncoding (1330/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
* ? NC_000913 225468 =2 (0.060)5 (0.150) 5/222 2.5 73.0% intergenic (+11/‑32) ileV/alaV tRNA‑Ile/tRNA‑Ala
?NC_000913 = 3427068 NA (NA)intergenic (‑35/+8) alaU/ileU tRNA‑Ala/tRNA‑Ile
* ? NC_000913 274620 =NA (NA)4 (0.120) 4/222 2.8 NA noncoding (530/1195 nt) IS5 repeat region
?NC_000913 274663 = NA (NA)noncoding (487/1195 nt) IS5 repeat region
* ? NC_000913 = 315520NA (NA)7 (0.210) 6/226 2.3 NA noncoding (292/1255 nt) IS3 repeat region
?NC_000913 = 315537 NA (NA)noncoding (309/1255 nt) IS3 repeat region
* ? NC_000913 = 120780512 (0.330)4 (0.130) 4/208 2.7 30.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 8 (0.250)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)39 (1.110) 36/232 0.1 100% 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
* ? NC_000913 1396531 =NA (NA)19 (0.550) 5/228 2.6 NA noncoding (488/1195 nt) IS5 repeat region
?NC_000913 = 1428264 NA (NA)noncoding (531/1196 nt) IS5 repeat region
* ? NC_000913 2066623 =11 (0.300)4 (0.110) 4/234 2.9 27.2% noncoding (731/1195 nt) IS5 repeat region
?NC_000913 2102181 = NA (NA)noncoding (763/1195 nt) IS5 repeat region
* ? NC_000913 = 230453612 (0.330)5 (0.140) 4/234 2.9 32.6% noncoding (120/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
?NC_000913 = 2304899 9 (0.250)noncoding (483/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
* ? NC_000913 = 345066828 (0.770)7 (0.200) 7/228 2.1 20.4% coding (697/822 nt) rplB 50S ribosomal subunit protein L2
?NC_000913 = 3450673 28 (0.810)coding (692/822 nt) rplB 50S ribosomal subunit protein L2
* ? NC_000913 = 3621980NA (NA)4 (0.120) 4/224 2.8 100% coding (2789/4236 nt) rhsB Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
?NC_000913 = 3622019 0 (0.000)coding (2828/4236 nt) rhsB Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
* ? NC_000913 = 41663726 (0.170)6 (0.170) 5/230 2.6 60.8% intergenic (+87/‑287) murI/rrsB glutamate racemase/16S ribosomal RNA of rrnB operon
?NC_000913 = 4166399 2 (0.060)intergenic (+114/‑260) murI/rrsB glutamate racemase/16S ribosomal RNA of rrnB operon
* ? NC_000913 = 445960324 (0.660)6 (0.180) 6/226 2.3 20.1% pseudogene (114/366 nt) cybC pseudogene, truncated cytochrome b562; cytochrome b(562)
?NC_000913 = 4459617 25 (0.730)pseudogene (128/366 nt) cybC pseudogene, truncated cytochrome b562; cytochrome b(562)