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 666,051 G→T A88E (GCG→GAG)  mrdB ← cell wall shape‑determining protein
RA 668,742 C→G E99Q (GAA→CAA)  rsfS ← ribosomal silencing factor
MC JC 1,677,217 Δ11 bp coding (677‑687/1533 nt) pntA ← pyridine nucleotide transhydrogenase, alpha subunit
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 JC 2,536,312 Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp coding (479‑484/510 nt) crr → glucose‑specific enzyme IIA component of PTS
RA 2,866,723 G→A R277* (CGA→TGA)  rpoS ← RNA polymerase, sigma S (sigma 38) factor
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 4,160,854 C→T intergenic (‑64/‑270) sthA ← / → fabR pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB
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

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 237108 237383 276 46 [44] [45] 47 [yafT] [yafT]
* * ÷ NC_000913 384602 385189 588 46 [45] [39] 54 [yaiS] [yaiS]
* * ÷ NC_000913 527130 529098 1969 46 [45] [44] 47 [rhsD]–[ybbD] [rhsD], ybbC, rhsH, [ybbD]
* * ÷ NC_000913 582740 584661 1922 46 [44] [45] 46 [ybcY]–appY [ybcY], ybcY, tfaX, appY
* * ÷ NC_000913 720758 721197 440 47 [42] [45] 46 [ybfK]–[kdpE] [ybfK], [kdpE]
* * ÷ NC_000913 997495 997930 436 46 [45] [44] 47 [ssuE]–[elfA] [ssuE], [elfA]
* * ÷ NC_000913 1092404 1093060 657 47 [45] [41] 51 [ycdT] [ycdT]
* * ÷ NC_000913 1196674 1198657 1984 50 [42] [38] 47 ymfD–ymfE ymfD, ymfE
* * ÷ NC_000913 1216154 1216737 584 46 [44] [45] 46 [ymgA]–ariR [ymgA], ariR
* * ÷ NC_000913 1299235 1300993 1759 46 [45] [43] 47 [ychE] [ychE]
* * ÷ NC_000913 1464915 1465419 505 46 [45] [41] 47 [paaY]–[ydbA] [paaY], ynbG, [ydbA]
* * ÷ NC_000913 1529934 1530568 635 47 [45] [45] 46 [rhsE]–[ydcD] [rhsE], [ydcD]
* * ÷ NC_000913 1544322 1545298 977 47 [43] [45] 51 yddK–[yddK] yddK, [yddK]
* * ÷ NC_000913 1812548 1813401 854 46 [43] [45] 46 [ydjO] [ydjO]
* * ÷ NC_000913 1957800 1958499 700 47 [44] [45] 47 [torY] [torY]
* * ÷ NC_000913 1978343 1979725 1383 46 [44] [45] 46 insB1–insA insB1, insA
* * ÷ NC_000913 2033460 2034126 667 48 [40] [45] 46 [yedR]–[yedS] [yedR], [yedS]
* * ÷ NC_000913 2057477 2058125 649 46 [42] [45] 47 [yeeN]–asnW [yeeN], asnW
* * ÷ NC_000913 2455559 2456234 676 47 [43] [39] 46 [yfcV] [yfcV]
* * ÷ NC_000913 2469060 2469940 881 46 [43] [45] 47 [gtrB]–[gtrS] [gtrB], [gtrS]
* * ÷ NC_000913 2628936 2629384 449 46 [45] [42] 46 [yfgF]–[yfgG] [yfgF], [yfgG]
* * ÷ NC_000913 2773236 2774060 825 46 [42] [44] 46 [yfjW] [yfjW]
* * ÷ NC_000913 2774320 2775352 1033 46 [42] [45] 46 [yfjW] [yfjW]
* * ÷ NC_000913 2785834 2786733 900 48 [45] [45] 46 [ileY]–[ygaQ] [ileY], [ygaQ]
* * ÷ NC_000913 2884174 2884471 298 47 [45] [43] 46 casA/ygcB CRISP RNA (crRNA) containing Cascade antiviral complex protein/Cascade complex anti‑viral R‑loop helicase‑annealase Cas3
* * ÷ NC_000913 3267908 3269744 1837 46 [45] [44] 46 [yhaB]–yhaC [yhaB], yhaC
* * ÷ NC_000913 3286965 3287496 532 48 [44] [45] 46 [agaI]–[yraH] [agaI], [yraH]
* * ÷ NC_000913 3423836–3424514 3424514 1–679 46 [45] [43] 46 [rrlD] [rrlD]
* * ÷ NC_000913 3623869 3624413 545 46 [44] [45] 46 yrhC–[yhhI] yrhC, [yhhI]
* * ÷ NC_000913 3634410 3634847 438 47 [45] [42] 46 [yhiL]–[yhiM] [yhiL], [yhiM]
* * ÷ NC_000913 3769178 3770276 1099 48 [44] [44] 46 [yibW]–[yibH] [yibW], yibV, yibV, yibU, yibU, [yibH]
* * ÷ NC_000913 3793333 3793787 455 46 [45] [43] 46 [yibB] [yibB]
* * ÷ NC_000913 3798474 3800393 1920 46 [45] [43] 46 [waaU]–[waaY] [waaU], waaZ, [waaY]
* * ÷ NC_000913 3800828 3801401 574 46 [42] [44] 46 [waaY]–[waaR] [waaY], [waaR]
* * ÷ NC_000913 4268450 4269397 948 47 [41] [43] 46 yjbS yjbS
* * ÷ NC_000913 4326734 4327309 576 46 [42] [45] 46 [yjdM]–[crfC] [yjdM], [crfC]
* * ÷ NC_000913 4476482 4477176 695 56 [44] [44] 46 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4541540 4542050 511 46 [44] [45] 47 [fimB]–[fimE] [fimB], [fimE]
* * ÷ NC_000913 4571582 4572484 903 48 [45] [45] 46 yjiS–[yjiT] yjiS, [yjiT]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =34 (0.310)71 (0.700) 54/460 0.6 71.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 25 (0.240)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780534 (0.310)59 (0.580) 47/460 0.9 67.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 25 (0.240)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related