breseq  version 0.27.1  revision 87c22d663cc3
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 668,742 C→G E99Q (GAA→CAA)  rsfS ← ribosomal silencing factor
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 2,513,351 C→A L104M (CTG→ATG)  nupC → nucleoside (except guanosine) transporter
JC 2,866,955 (TTGCTCT)1→2 coding (597/993 nt) rpoS ← RNA polymerase, sigma S (sigma 38) factor
MC JC 3,440,071 Δ20 bp coding (940‑959/990 nt) rpoA ← RNA polymerase, alpha 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
RA 3,815,808 (A)8→7 intergenic (‑40/+26) pyrE ← / ← rph orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
MC JC 4,233,804 1557 bp→83 bp coding (47‑1603/1650 nt) pgi → glucosephosphate isomerase
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,400,429 A→C N48H (AAC→CAC)  hfq → global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication
JC JC 4,547,304 Δ2 bp :: IS186 (+) +7 bp :: Δ1 bp coding (2209‑2215/2637 nt) fimD → fimbrial usher outer membrane porin protein; FimCD chaperone‑usher

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 331560 332244 685 34 [33] [32] 34 betT/yahA choline transporter of high affinity/c‑di‑GMP‑specific phosphodiesterase
* * ÷ NC_000913 527175 528051 877 36 [30] [33] 34 [rhsD]–[rhsH] [rhsD], ybbC, [rhsH]
* * ÷ NC_000913 528187 529114 928 34 [33] [33] 35 [rhsH]–[ybbD] [rhsH], [ybbD]
* * ÷ NC_000913 568516 569116 601 36 [33] [33] 36 [emrE]–[ybcK] [emrE], [ybcK]
* * ÷ NC_000913 582704 584724 2021 34 [32] [32] 36 [ybcY]–[ompT] [ybcY], ybcY, tfaX, appY, [ompT]
* * ÷ NC_000913 720775 721191 417 34 [33] [33] 34 [ybfK]–[kdpE] [ybfK], [kdpE]
* * ÷ NC_000913 752686 753224 539 34 [32] [30] 35 [ybgD]–[gltA] [ybgD], [gltA]
* * ÷ NC_000913 954479 954849 371 34 [33] [33] 36 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ NC_000913 997453 997989 537 34 [33] [33] 35 [ssuE]–[elfA] [ssuE], [elfA]
* * ÷ NC_000913 1196725 1197918 1194 34 [33] [32] 34 ymfD–[ymfE] ymfD, [ymfE]
* * ÷ NC_000913 1211040 1212834 1795 36 [32] [31] 34 [mcrA]–[ycgX] [mcrA], icdC, iraM, [ycgX]
* * ÷ NC_000913 1216174 1216722 549 34 [32] [33] 36 [ymgA]–ariR [ymgA], ariR
* * ÷ NC_000913 1526697 1527845 1149 35 [33] [33] 35 [yncG]–yncH [yncG], yncH
* * ÷ NC_000913 1529954 1530505 552 35 [33] [33] 34 [ydcD] [ydcD]
* * ÷ NC_000913 1586467 1586851 385 35 [32] [33] 35 [ydeP]–[ydeQ] [ydeP], [ydeQ]
* * ÷ NC_000913 1598066 1598482 417 34 [33] [33] 34 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ NC_000913 1624514 1624828 315 35 [32] [33] 36 [ydeJ] [ydeJ]
* * ÷ NC_000913 1978342 1979749 1408 37 [33] [33] 34 insB1–insA insB1, insA
* * ÷ NC_000913 2033460 2034123 664 34 [33] [33] 34 [yedR]–[yedS] [yedR], [yedS]
* * ÷ NC_000913 2056592 2056815 224 38 [33] [32] 34 amn/yeeN AMP nucleosidase/UPF0082 family protein
* * ÷ NC_000913 2068411 2068676 266 34 [33] [32] 34 [yoeH]–[yoeA] [yoeH], [yoeA]
* * ÷ NC_000913 2103302 2104304 1003 35 [33] [33] 34 [wbbL]–[wbbK] [wbbL], [wbbK]
* * ÷ NC_000913 2385649 2386006 358 34 [32] [33] 34 [yfbK]–[yfbL] [yfbK], [yfbL]
* * ÷ NC_000913 2455569 2456184 616 36 [33] [33] 35 [yfcV] [yfcV]
* * ÷ NC_000913 2469055 2469861 807 36 [31] [33] 35 [gtrB]–[gtrS] [gtrB], [gtrS]
* * ÷ NC_000913 2470040 2470496 457 34 [28] [28] 38 [gtrS] [gtrS]
* * ÷ NC_000913 2784285 2785549 1265 34 [32] [33] 34 [ypjC] [ypjC]
* * ÷ NC_000913 2785894 2786805 912 35 [33] [32] 34 [ygaQ] [ygaQ]
* * ÷ NC_000913 3267071 3267609 539 34 [33] [33] 34 tdcR tdcR
* * ÷ NC_000913 3267903 3269733 1831 34 [33] [33] 34 [yhaB]–yhaC [yhaB], yhaC
* * ÷ NC_000913 3286960 3287498 539 34 [33] [33] 34 [agaI]–[yraH] [agaI], [yraH]
* * ÷ NC_000913 3360727 3361225 499 39 [33] [33] 34 [gltF] [gltF]
* * ÷ NC_000913 3423846–3424467 3424467 1–622 34 [33] [33] 34 [rrlD] [rrlD]
* * ÷ NC_000913 3455276 3455895 620 34 [33] [33] 34 [gspA]–[gspC] [gspA], [gspC]
* * ÷ NC_000913 3582527 3584896 2370 34 [33] [33] 34 [yhhZ]–[yrhB] [yhhZ], yrhA, insA, insB1, yrhA, [yrhB]
* * ÷ NC_000913 3633402 3634358 957 35 [33] [33] 34 yhiL pseudogene, DUF4049 family protein
* * ÷ NC_000913 3653277 3653973 697 34 [32] [31] 34 [yhiS]–[slp] [yhiS], [slp]
* * ÷ NC_000913 3665794 3666098 305 34 [33] [30] 39 [gadX] [gadX]
* * ÷ NC_000913 3751831 3752257 427 37 [31] [32] 34 [yiaT]–[yiaU] [yiaT], [yiaU]
* * ÷ NC_000913 3769364 3770307 944 34 [32] [32] 34 [yibV]–[yibH] [yibV], yibV, yibU, yibU, [yibH]
* * ÷ NC_000913 3793345 3793799 455 34 [33] [32] 38 [yibB] [yibB]
* * ÷ NC_000913 3796881 3800377 3497 35 [33] [28] 34 [waaC]–[waaY] [waaC], waaL, waaU, waaZ, [waaY]
* * ÷ NC_000913 3804105 3805298 1194 34 [31] [33] 34 [waaB]–[waaP] [waaB], waaS, [waaP]
* * ÷ NC_000913 3836569 3836855 287 36 [33] [33] 34 yicT/setC pseudogene/putative arabinose efflux transporter
* * ÷ NC_000913 4251367 4252097 731 34 [33] [33] 34 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ NC_000913 4475552 4476160 609 34 [33] [33] 34 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4541534 4542090 557 34 [33] [32] 34 [fimB]–[fimE] [fimB], [fimE]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =8 (0.100)71 (0.970) 53/464 0.2 90.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 7 (0.100)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078058 (0.100)72 (0.980) 50/464 0.2 90.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 7 (0.100)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related