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 insB9–[crl] insB9, insA9, [crl]
MC JC 1,299,499 Δ1,199 bp insH21 insH21
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA5 ← / → uspC IS1 family protein InsA/universal stress protein C
RA 2,173,363 Δ2 bp intergenic (‑490/+918) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
RA 3,560,455 +G intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 4,106,201 C→T Q128* (CAG→TAG)  cpxP → periplasmic protein CpxP
RA 4,296,381 +GC intergenic (+587/+55) 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 283360 283417 58 2 [0] [1] 2 yagF D‑xylonate dehydratase
* * ÷ NC_000913 283724 283995 272 2 [0] [0] 2 yagF D‑xylonate dehydratase
* * ÷ NC_000913 284057 284251 195 2 [0] [0] 2 yagF D‑xylonate dehydratase
* * ÷ NC_000913 287563 287848 286 3 [1] [1] 2 yagH putative xylosidase/arabinosidase
* * ÷ NC_000913 288373 288477 105 2 [1] [1] 2 [yagH]–[xynR] [yagH],[xynR]
* * ÷ NC_000913 523875 523894 20 2 [0] [0] 2 rhsD protein RhsD
* * ÷ NC_000913 730147 730209–730176 30–63 2 [1] [0] 2 rhsC rhs element protein RhsC
* * ÷ NC_000913 915194 915212 19 2 [0] [1] 2 lysO/aqpZ L‑lysine/thialysine exporter/water channel AqpZ
* * ÷ NC_000913 1558736 1558787 52 3 [1] [0] 2 ddpD putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpD
* * ÷ NC_000913 1731465 1731466 2 2 [0] [0] 2 lhr ATP‑dependent helicase Lhr
* * ÷ NC_000913 1978503–1979269 1979277 9–775 29 [0] [1] 3 insB5–insA5 insB5,insA5
* * ÷ NC_000913 2229162 2229211 50 2 [1] [1] 2 yohP/dusC putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase
* * ÷ NC_000913 2530731 2530833 103 3 [1] [0] 2 zipA cell division protein ZipA
* * ÷ NC_000913 2530929 2530946 18 2 [0] [0] 3 zipA cell division protein ZipA
* * ÷ NC_000913 2791339 2791396 58 2 [0] [1] 3 gabD succinate‑semialdehyde dehydrogenase (NADP(+)) GabD
* * ÷ NC_000913 2791843 2791932 90 2 [1] [1] 2 gabD succinate‑semialdehyde dehydrogenase (NADP(+)) GabD
* * ÷ NC_000913 3423915–3424233 3424397–3424241 9–483 2 [1] [1] 2 rrlD 23S ribosomal RNA
* * ÷ NC_000913 4314971 4315053 83 2 [1] [0] 2 phnP 5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
* * ÷ NC_000913 4315774 4315786 13 2 [0] [0] 2 phnN ribose 1,5‑bisphosphate phosphokinase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =6 (0.260)18 (0.870) 15/350 0.4 68.6% coding (290/630 nt) ycfK protein StfP
?NC_000913 1209619 = 11 (0.530)intergenic (‑500/‑66) tfaE/pinE putative tail fiber assembly protein TfaE/site‑specific DNA recombinase
* ? NC_000913 = 12078056 (0.260)6 (0.290) 6/350 1.5 42.1% coding (305/630 nt) ycfK protein StfP
?NC_000913 = 1209602 11 (0.530)intergenic (‑483/‑83) tfaE/pinE putative tail fiber assembly protein TfaE/site‑specific DNA recombinase
* ? NC_000913 = 19785020 (0.000)29 (1.330) 26/366 0.1 100% intergenic (‑305/+16) flhD/insB5 DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA5/uspC IS1 family protein InsA/universal stress protein C
* ? NC_000913 = 1979270NA (NA)17 (0.750) 12/382 0.8 32.1% noncoding (1/768 nt) IS1 repeat region
?NC_000913 = 3853475 36 (1.590)intergenic (‑218/‑78) istR/tisB small RNA IstR‑2/membrane‑depolarizing toxin TisB