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]
RA 263,603 G→A 18.8% Q23* (CAA→TAA)  ykfI ← CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system
RA 292,571 G→T 12.1% Y126* (TAC→TAA)  yagK ← CP4‑6 prophage; uncharacterized protein YagK
RA 819,360 G→T 24.0% L22L (CTG→CTT)  moaE → molybdopterin synthase catalytic subunit
MC JC 1,299,499 Δ1,199 bp 100% insH21 insH21
RA 1,517,532 C→T 18.4% F48F (TTC→TTT)  ortT → orphan toxin OrtT
RA 1,547,149 C→T 17.4% T7T (ACG→ACA)  yddG ← aromatic amino acid exporter
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 2,173,361 Δ2 bp 100% pseudogene (917‑918/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,383,257 Δ1 bp 10.3% coding (545/1212 nt) elaD → protease ElaD
RA 3,410,763 G→A 16.7% G162S (GGC→AGC)  dusB → tRNA‑dihydrouridine synthase B
RA 3,504,511 T→C 17.4% Y154H (TAT→CAT)  frlR → putative DNA‑binding transcriptional regulator FrlR
RA 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 4,183,378 T→C 31.0% S712P (TCC→CCC)  rpoB → RNA polymerase subunit beta
RA 4,186,532 A→G 28.6% K395E (AAA→GAA)  rpoC → RNA polymerase subunit beta'
RA 4,296,060 C→T 40.0% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
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 283918 284001 84 2 [1] [1] 2 yagF CP4‑6 prophage; D‑xylonate dehydratase
* * ÷ NC_000913 287638 287671 34 2 [1] [1] 2 yagH CP4‑6 prophage; putative xylosidase/arabinosidase
* * ÷ NC_000913 776779 776799 21 2 [1] [1] 2 tolA Tol‑Pal system protein TolA
* * ÷ NC_000913 913735 913755 21 2 [1] [1] 2 hcp protein S‑nitrosylase
* * ÷ NC_000913 980657 980669 13 3 [0] [0] 4 mukB chromosome partitioning protein MukB
* * ÷ NC_000913 1043866 1043897 32 2 [1] [1] 3 etk protein‑tyrosine kinase Etk
* * ÷ NC_000913 1137575 1137582 8 3 [0] [0] 2 flgJ putative peptidoglycan hydrolase FlgJ
* * ÷ NC_000913 1393303 1393315 13 2 [1] [1] 2 mppA murein tripeptide ABC transporter periplasmic binding protein
* * ÷ NC_000913 2098515 2098533 19 2 [1] [1] 2 ugd UDP‑glucose 6‑dehydrogenase
* * ÷ NC_000913 2164409 2164420 12 4 [1] [1] 2 baeR DNA‑binding transcriptional activator BaeR
* * ÷ NC_000913 2178606 2178608 3 3 [0] [0] 3 fbaB/yegT fructose‑bisphosphate aldolase class I/putative transporter YegT
* * ÷ NC_000913 2183220 2183250 31 2 [1] [1] 2 yegX putative hydrolase
* * ÷ NC_000913 2271801 2271804 4 2 [0] [0] 2 pdeN putative c‑di‑GMP phosphodiesterase PdeN
* * ÷ NC_000913 2619127 2619143 17 2 [1] [0] 3 uraA hypothetical protein
* * ÷ NC_000913 3043656 3043668 13 3 [0] [0] 5 [bglA] [bglA]
* * ÷ NC_000913 3423824–3424234 3424404–3424239 6–581 2 [1] [1] 2 [rrlD] [rrlD]
* * ÷ NC_000913 3468868 3468881 14 2 [1] [0] 2 chiA endochitinase
* * ÷ NC_000913 3556145 3556156 12 2 [1] [1] 7 rtcA RNA 3'‑terminal phosphate cyclase
* * ÷ NC_000913 4003241 4003245 5 2 [0] [1] 2 yigG/rarD inner membrane protein/putative transporter RarD
* * ÷ NC_000913 4511478 4511490 13 2 [1] [1] 2 fecD ferric citrate ABC transporter membrane subunit FecD
* * ÷ NC_000913 4565643 4565676 34 2 [1] [1] 3 yjiM putative dehydratase subunit

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =7 (0.390)16 (1.020) 13/232 NT 75.9% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 4 (0.250)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12078057 (0.390)16 (1.020) 16/232 NT 75.9% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 4 (0.250)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment