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
MC JC 257,908 Δ776 bp 100% insB9–[crl] insB9, insA9, [crl]
JC JC 622,244 IS5 (–) +4 bp 33.3% intergenic (‑55/‑53) fepD ← / → entS ferric enterobactin ABC transporter membrane subunit FebD/enterobactin exporter EntS
RA 1,184,432 T→A 15.8% I5F (ATT→TTT)  potB ← spermidine preferential ABC transporter membrane subunit PotB
MC JC 1,299,499 Δ1,199 bp 100% insH21 insH21
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA‑5 ← / → uspC IS1 protein InsA/universal stress protein C
RA 2,173,361 Δ2 bp 100% pseudogene (917‑918/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
JC 3,277,257 +CATTCAA 20.0% coding (256/336 nt) prlF → antitoxin PrlF
RA 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,510,928 A→T 52.0% L177Q (CTG→CAG)  fecE ← ferric citrate ABC transporter ATP binding subunit
RA 4,515,480 C→T 100% G400S (GGC→AGC)  fecA ← ferric citrate outer membrane transporter

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 299928 300006 79 3 [1] [1] 2 paoC aldehyde dehydrogenase: molybdenum cofactor‑binding subunit
* * ÷ NC_000913 433060 433078 19 2 [1] [1] 2 nrdR NrdR transcriptional repressor
* * ÷ NC_000913 759214 759238 25 3 [1] [0] 2 sucA subunit of E1(0) component of 2‑oxoglutarate dehydrogenase
* * ÷ NC_000913 1231467 1231514 48 2 [1] [1] 3 umuC DNA polymerase V catalytic protein
* * ÷ NC_000913 1257007 1257064 58 2 [0] [1] 2 ychF redox‑responsive ATPase YchF
* * ÷ NC_000913 1415685 1415708 24 2 [1] [1] 2 recE Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific
* * ÷ NC_000913 1425448 1425453 6 2 [0] [1] 2 ynaK Rac prophage; ParB‑like nuclease domain‑containing protein YnaK
* * ÷ NC_000913 1484460 1484503 44 2 [1] [0] 2 hrpA ATP‑dependent RNA helicase HrpA
* * ÷ NC_000913 1669652 1669659 8 2 [1] [0] 2 ynfL/ynfM putative DNA‑binding transcriptional regulator/putative transporter YnfM
* * ÷ NC_000913 1812787 1812802 16 2 [1] [1] 2 ydjO protein YdjO
* * ÷ NC_000913 1963231 1963256 26 2 [1] [1] 2 flhA flagellar biosynthesis protein FlhA
* * ÷ NC_000913 1978503–1979266 1979277 12–775 12 [0] [1] 2 insB‑5–insA‑5 insB‑5,insA‑5
* * ÷ NC_000913 1991934 1991975 42 2 [1] [0] 2 cysT tRNA‑Cys
* * ÷ NC_000913 2023345 2023361 17 2 [1] [1] 2 fliR flagellar biosynthesis protein FliR
* * ÷ NC_000913 2091623 2091642 20 2 [0] [1] 2 hisD histidinal/histidinol dehydrogenase
* * ÷ NC_000913 2254561 2254585 25 2 [1] [1] 2 rihB pyrimidine‑specific ribonucleoside hydrolase RihB
* * ÷ NC_000913 2432123 2432144 22 2 [0] [1] 2 folC bifunctional folylpolyglutamate synthetase/dihydrofolate synthetase
* * ÷ NC_000913 2466617 2466623 7 2 [1] [1] 3 intS CPS‑53 (KpLE1) prophage; prophage CPS‑53 integrase
* * ÷ NC_000913 2481110 2481136 27 2 [1] [1] 2 emrY tripartite efflux pump membrane subunit EmrY
* * ÷ NC_000913 2617022 2617060 39 2 [0] [1] 2 bepA beta‑barrel assembly‑enhancing protease
* * ÷ NC_000913 2644735 2644738 4 2 [1] [1] 2 ndk nucleoside diphosphate kinase
* * ÷ NC_000913 2763728 2763760 33 2 [1] [1] 2 abpA CP4‑57 prophage; anti‑bacteriophage protein
* * ÷ NC_000913 3423754–3424234 3424509–3424238 5–756 2 [1] [1] 2 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3438349 3438371 23 2 [1] [0] 3 mscL large conductance mechanosensitive channel
* * ÷ NC_000913 3738810 3738810 1 2 [0] [0] 2 malS alpha‑amylase
* * ÷ NC_000913 3758456 3758496 41 2 [1] [1] 2 selB selenocysteyl‑tRNA‑specific translation elongation factor
* * ÷ NC_000913 3814062 3814082 21 2 [1] [1] 2 dut deoxyuridine triphosphatase
* * ÷ NC_000913 4136412 4136426 15 2 [1] [0] 2 yijE cystine exporter
* * ÷ NC_000913 4183849 4183871 23 2 [1] [1] 2 rpoB RNA polymerase subunit beta
* * ÷ NC_000913 4263183 4263195 13 3 [1] [1] 2 pspG/qorA phage shock protein G/putative quinone oxidoreductase 1
* * ÷ NC_000913 4282893 4282943 51 2 [1] [1] 2 yjcF pentapeptide repeat‑containing protein YjcF
* * ÷ NC_000913 4314692 4314710 19 2 [0] [0] 2 phnP 5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
* * ÷ NC_000913 4342503 4342506 4 2 [0] [1] 2 melA alpha‑galactosidase
* * ÷ NC_000913 4400108 4400136 29 2 [1] [1] 2 miaA tRNA dimethylallyltransferase
* * ÷ NC_000913 4417516 4417596 81 2 [1] [1] 2 yjfP carboxylesterase
* * ÷ NC_000913 4431692 4431718 27 2 [1] [1] 2 ytfE iron‑sulfur cluster repair protein YtfE

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 502521 =7 (0.440)64 (4.180) 49/354 NT 85.5% coding (718/1677 nt) ybaL putative transporter YbaL
?NC_000913 = 556662 15 (0.980)coding (212/213 nt) ybcJ putative RNA‑binding protein YbcJ
* ? NC_000913 1207790 =6 (0.380)7 (0.480) 6/336 NT 54.9% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 6 (0.410)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12078056 (0.380)14 (0.960) 12/336 NT 70.9% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 6 (0.410)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 19785020 (0.000)12 (0.790) 11/352 NT 100% intergenic (‑305/+16) flhD/insB‑5 DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA‑5/uspC IS1 protein InsA/universal stress protein C
* ? NC_000913 = 2290113NA (NA)20 (1.260) 16/366 NT 66.7% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 2629045 10 (0.630)intergenic (‑107/‑245) pdeF/yfgG cyclic di‑GMP phosphodiesterase PdeF/protein YfgG