breseq  version 0.26.0  
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% [crl] [crl]
JC JC 573,890 IS5 (–) +4 bp 88.9% intergenic (+20/‑63) ylcG → / → quuD uncharacterized protein, DLP12 prophage/DLP12 prophage; putative antitermination protein
RA 657,541 G→T 83.5% intergenic (+40/+14) cspE → / ← flc constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein
RA 1,220,733 T→C 5.7% pseudogene (1133/2574 nt) ycgH → pseudogene; putative ATP‑binding component of a transport system
RA 1,286,965 A→G 9.3% intergenic (+439/+122) narI → / ← tpr nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
RA 1,286,974 C→T 6.7% intergenic (+448/+113) narI → / ← tpr nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
RA 1,529,218 C→T 100% pseudogene (1317/2037 nt) rhsE → pseudogene, Rhs family
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,304,537 A→G 9.0% intergenic (+144/+571) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,540 C→T 5.1% intergenic (+147/+568) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,549 C→T 5.4% intergenic (+156/+559) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
JC 2,305,072 Δ53 bp 2.1% [mqo] [mqo]
RA 2,911,534 Δ1 bp 88.4% coding (2118/2235 nt) relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase
RA 3,560,455 +G 100% 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 4,187,507 A→C 100% N720H (AAC→CAC)  rpoC → RNA polymerase, beta prime subunit
RA 4,296,190 A→G 16.7% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 14.3% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 35.3% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 23.4% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,303 A→G 8.2% intergenic (+509/+133) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,304 A→C 12.9% intergenic (+510/+132) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380 +CG 100% intergenic (+586/+56) 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 156825 157407 583 46 [44] [44] 45 [yadN]–[folK] [yadN], [folK]
* * ÷ NC_000913 238050 238960 911 48 [44] [44] 46 [yafT]–[yafU] [yafT], ykfM, [yafU]
* * ÷ NC_000913 246105 246733 629 49 [43] [41] 45 [yafQ]–[yafL] [yafQ], dinJ, [yafL]
* * ÷ NC_000913 318380 318785 406 45 [44] [44] 45 [rclB]–[rclA] [rclB], [rclA]
* * ÷ NC_000913 384578 385202 625 46 [43] [44] 47 [yaiS] [yaiS]
* * ÷ NC_000913 522843 523281 439 50 [37] [44] 45 [rhsD] [rhsD]
* * ÷ NC_000913 527187 529248 2062 45 [41] [44] 45 [rhsD]–ybbD [rhsD], ybbC, rhsH, ybbD
* * ÷ NC_000913 537427 537768 342 45 [43] [43] 45 [glxR]–[ybbW] [glxR], [ybbW]
* * ÷ NC_000913 568547 569135 589 45 [44] [43] 45 [emrE]–[ybcK] [emrE], [ybcK]
* * ÷ NC_000913 569870 570980 1111 46 [44] [44] 45 [ybcK]–[ybcL] [ybcK], [ybcL]
* * ÷ NC_000913 578875 579964 1090 52 [44] [44] 47 [borD]–[ybcW] [borD], ybcV, [ybcW]
* * ÷ NC_000913 582629 584777 2149 47 [44] [44] 45 [ybcY]–[ompT] [ybcY], ybcY, tfaX, appY, [ompT]
* * ÷ NC_000913 651909 652366 458 45 [43] [43] 45 [citA] [citA]
* * ÷ NC_000913 707877 708323 447 45 [44] [35] 45 glnS/chiP glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars
* * ÷ NC_000913 720795 721159 365 47 [39] [42] 45 [ybfK]–[kdpE] [ybfK], [kdpE]
* * ÷ NC_000913 770748 771312 565 45 [42] [44] 46 mngB/cydA alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
* * ÷ NC_000913 997488 997946 459 46 [42] [44] 47 [ssuE]–[elfA] [ssuE], [elfA]
* * ÷ NC_000913 1196672 1198797 2126 45 [43] [44] 45 ymfD–[lit] ymfD, ymfE, [lit]
* * ÷ NC_000913 1215477 1215830 354 45 [44] [44] 45 [ycgZ] [ycgZ]
* * ÷ NC_000913 1230157 1230749 593 46 [44] [42] 45 [hlyE] [hlyE]
* * ÷ NC_000913 1255905 1256442 538 45 [44] [42] 45 [ycgV] [ycgV]
* * ÷ NC_000913 1299182 1301024 1843 45 [44] [44] 45 [ychE] [ychE]
* * ÷ NC_000913 1423608 1424552 945 46 [41] [44] 49 [rzpR]–[trkG] [rzpR], [trkG]
* * ÷ NC_000913 1464977 1465429 453 46 [42] [42] 45 [paaY]–[ydbA] [paaY], ynbG, [ydbA]
* * ÷ NC_000913 1526661 1527752 1092 47 [42] [42] 45 [yncG]–yncH [yncG], yncH
* * ÷ NC_000913 1529894 1530666 773 45 [43] [42] 45 [rhsE]–[yncI] [rhsE], ydcD, [yncI]
* * ÷ NC_000913 1544274 1545300 1027 48 [42] [43] 45 yddK–[yddK] yddK, [yddK]
* * ÷ NC_000913 1545832 1546418 587 45 [43] [44] 46 [yddL]–[yddG] [yddL], [yddG]
* * ÷ NC_000913 1640569 1641263 695 47 [41] [43] 47 [essQ] [essQ]
* * ÷ NC_000913 1812558 1813409 852 47 [43] [42] 45 [ydjO] [ydjO]
* * ÷ NC_000913 1978259 1979749 1491 45 [43] [43] 45 insB1–insA insB1, insA
* * ÷ NC_000913 2011148 2012514 1367 45 [44] [44] 46 yedN–[intG] yedN, yedN, yedN, [intG]
* * ÷ NC_000913 2033445 2034200 756 45 [44] [42] 45 [yedR]–[yedS] [yedR], [yedS]
* * ÷ NC_000913 2067905 2068694 790 48 [43] [44] 46 yoeH–[yoeA] yoeH, [yoeA]
* * ÷ NC_000913 2103226 2104257 1032 45 [42] [44] 45 [wbbL]–[wbbK] [wbbL], [wbbK]
* * ÷ NC_000913 2105038 2107493 2456 47 [44] [44] 45 [wbbJ]–[glf] [wbbJ], wbbI, wbbH, [glf]
* * ÷ NC_000913 2107997 2108638 642 46 [43] [43] 45 [glf]–[wzxB] [glf], [wzxB]
* * ÷ NC_000913 2168170 2168566 397 45 [43] [44] 46 [yegR] [yegR]
* * ÷ NC_000913 2192089 2192558 470 45 [42] [43] 45 [yehD]–[yehE] [yehD], [yehE]
* * ÷ NC_000913 2303547 2303922 376 45 [44] [42] 46 [eco] [eco]
* * ÷ NC_000913 2344141 2344713 573 45 [43] [39] 45 [yfaL] [yfaL]
* * ÷ NC_000913 2385635 2386036 402 45 [44] [43] 45 [yfbK]–[yfbL] [yfbK], [yfbL]
* * ÷ NC_000913 2388314 2388752 439 49 [43] [35] 45 [yfbN]–[yfbO] [yfbN], [yfbO]
* * ÷ NC_000913 2455570 2456217 648 45 [44] [42] 47 [yfcV] [yfcV]
* * ÷ NC_000913 2469007 2470757 1751 48 [44] [44] 45 [gtrB]–gtrS [gtrB], gtrS
* * ÷ NC_000913 2590920 2591327 408 45 [44] [44] 45 [yffB] [yffB]
* * ÷ NC_000913 2628847 2629305 459 47 [42] [44] 45 [yfgF]–[yfgG] [yfgF], [yfgG]
* * ÷ NC_000913 2759852 2760515 664 45 [42] [44] 45 [yfjI] [yfjI]
* * ÷ NC_000913 2773205 2774118 914 47 [42] [44] 46 [yfjW] [yfjW]
* * ÷ NC_000913 2774325 2775541 1217 45 [43] [41] 46 [yfjW] [yfjW]
* * ÷ NC_000913 2784206 2785667 1462 50 [44] [43] 45 [ypjC] [ypjC]
* * ÷ NC_000913 2798485 2799194 710 46 [42] [43] 46 [stpA]–[alaE] [stpA], [alaE]
* * ÷ NC_000913 2903477 2904069 593 45 [44] [44] 45 ygcE/queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
* * ÷ NC_000913 2904347 2904820 474 45 [43] [44] 46 [queE] [queE]
* * ÷ NC_000913 2989235 2990036 802 45 [40] [43] 45 [yqeI]–[yqeK] [yqeI], yqeJ, yqeL, [yqeK]
* * ÷ NC_000913 2990571 2991590 1020 45 [43] [44] 48 [ygeF]–[ygeG] [ygeF], ygeF, [ygeG]
* * ÷ NC_000913 2991769 2993004 1236 49 [43] [43] 47 [ygeH] [ygeH]
* * ÷ NC_000913 2993388 2994468 1081 45 [44] [43] 45 [ygeH]–[ygeK] [ygeH], ygeI, pbl, pbl, [ygeK]
* * ÷ NC_000913 3087950 3088268 319 47 [44] [41] 48 metK/galP S‑adenosylmethionine synthetase/D‑galactose transporter
* * ÷ NC_000913 3136335 3136677 343 45 [44] [43] 45 [pitB]–[gss] [pitB], [gss]
* * ÷ NC_000913 3185099 3185530 432 48 [44] [44] 45 [yqiC]–[ygiL] [yqiC], [ygiL]
* * ÷ NC_000913 3267032 3267566 535 45 [43] [44] 45 [tdcA]–[tdcR] [tdcA], [tdcR]
* * ÷ NC_000913 3267876 3269766 1891 45 [43] [44] 45 [yhaB]–yhaC [yhaB], yhaC
* * ÷ NC_000913 3286904 3287507 604 45 [37] [44] 45 [agaI]–[yraH] [agaI], [yraH]
* * ÷ NC_000913 3385270 3385507 238 45 [44] [44] 45 argR/yhcN l‑arginine‑responsive arginine metabolism regulon transcriptional regulator/cadmium and peroxide resistance protein, stress‑induced
* * ÷ NC_000913 3455330 3455908 579 45 [43] [44] 45 [gspA]–[gspC] [gspA], [gspC]
* * ÷ NC_000913 3581626 3582286 661 45 [44] [41] 45 [yhhY]–[yhhZ] [yhhY], [yhhZ]
* * ÷ NC_000913 3582430 3583420 991 47 [39] [31] 46 [yhhZ]–yrhA [yhhZ], yrhA
* * ÷ NC_000913 3583465–3584195 3584941 747–1477 45 [43] [42] 47 insA–[yrhB] insA, insB1, yrhA, [yrhB]
* * ÷ NC_000913 3623180 3624440 1261 45 [44] [44] 45 [rhsB]–[yhhI] [rhsB], yhhH, yrhC, [yhhI]
* * ÷ NC_000913 3631686 3634847 3162 47 [44] [43] 46 [yhiJ]–[yhiM] [yhiJ], yhiL, yhiL, [yhiM]
* * ÷ NC_000913 3751791 3752342 552 45 [43] [44] 45 [yiaT]–[yiaU] [yiaT], [yiaU]
* * ÷ NC_000913 3769175 3770230 1056 50 [43] [43] 45 [yibW]–yibU [yibW], yibV, yibV, yibU, yibU
* * ÷ NC_000913 3793335 3793804 470 47 [43] [42] 45 [yibB] [yibB]
* * ÷ NC_000913 3796872 3800467 3596 47 [42] [44] 46 [waaC]–[waaY] [waaC], waaL, waaU, waaZ, [waaY]
* * ÷ NC_000913 3801692 3803334 1643 48 [44] [44] 45 [waaR]–[waaB] [waaR], waaO, [waaB]
* * ÷ NC_000913 3804049 3805235 1187 45 [44] [43] 45 [waaB]–[waaP] [waaB], waaS, [waaP]
* * ÷ NC_000913 3985992 3986385 394 45 [43] [40] 46 [aslA] [aslA]
* * ÷ NC_000913 4002516 4003355 840 45 [44] [44] 45 [yigF]–[rarD] [yigF], yigG, [rarD]
* * ÷ NC_000913 4221578 4222741 1164 45 [42] [34] 49 [arpA] [arpA]
* * ÷ NC_000913 4251387 4252049 663 45 [40] [44] 46 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ NC_000913 4268412 4269388 977 45 [41] [44] 47 yjbS yjbS
* * ÷ NC_000913 4326744 4327189 446 46 [44] [44] 45 [crfC] [crfC]
* * ÷ NC_000913 4475334 4476224 891 45 [44] [44] 45 [yjgL] [yjgL]
* * ÷ NC_000913 4476430 4477229 800 47 [44] [41] 48 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4497871 4499438–4498187 317–1568 45 [44] [43] 45 [intB]–[insD1] [intB], insC1, [insD1]
* * ÷ NC_000913 4542494 4543003 510 47 [44] [43] 45 [fimE] [fimE]
* * ÷ NC_000913 4556312 4556824 513 48 [36] [44] 45 [yjiC] [yjiC]
* * ÷ NC_000913 4571605 4572511 907 45 [42] [43] 45 yjiS–[yjiT] yjiS, [yjiT]

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 41482674 (0.680)3 (0.030) 3/524 NT 4.1% coding (928/3147 nt) sbcC exonuclease, dsDNA, ATP‑dependent
?NC_000913 = 414832 69 (0.660)coding (922/3147 nt) sbcC exonuclease, dsDNA, ATP‑dependent
* ? NC_000913 1207790 =28 (0.260)45 (0.440) 36/506 NT 59.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 36 (0.350)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780525 (0.230)46 (0.450) 39/506 NT 60.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 36 (0.350)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 19785020 (0.000)3 (0.030) 3/522 NT 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein
* ? NC_000913 4335640 =123 (1.140)3 (0.030) 3/510 NT 2.5% intergenic (‑50/+54) eptA/adiC lipid A phosphoethanolamine transferase/arginine:agmatine antiporter
?NC_000913 4335670 = 115 (1.120)intergenic (‑80/+24) eptA/adiC lipid A phosphoethanolamine transferase/arginine:agmatine antiporter