mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 29,252 | G→A | intergenic (+57/‑399) | dapB → / → carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl‑phosphate synthetase small subunit |
| RA | 148,502 | G→A | I98I (ATC→ATT) | panC ← | pantothenate synthetase |
| RA | 209,247 | G→A | L209L (CTG→CTA) | accA → | acetyl‑CoA carboxyltransferase subunit alpha |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 320,156 | T→C | intergenic (‑155/‑71) | rclA ← / → rclR | cupric reductase RclA/DNA‑binding transcriptional activator RclR |
| JC JC | 332,112 | IS2 (–) +5 bp | intergenic (+236/‑255) | yahV → / → pdeL | protein YahV/DNA‑binding transcriptional regulator/c‑di‑GMP phosphodiesterase PdeL |
| RA | 405,638 | T→C | K3E (AAG→GAG) | proC ← | pyrroline‑5‑carboxylate reductase |
| RA | 495,201 | A→T | K28* (AAA→TAA) | htpG → | chaperone protein HtpG |
| RA | 495,211 | T→C | F31S (TTC→TCC) | htpG → | chaperone protein HtpG |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 564,280 | IS2 (+) +5 bp | coding (197‑201/633 nt) | fimZ ← | putative LuxR family transcriptional regulator FimZ |
| RA | 581,072 | G→A | G80E (GGG→GAG) | nohD → | putative DNA‑packaging protein NohD |
| MC JC | 681,461 | Δ6,390 bp | IS5‑mediated | [djlC]–gltI | [djlC], hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 727,250 | C→T | G495R (GGG→AGG) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 736,715 | C→T | intergenic (+16/‑1377) | ybfQ → / → ybfD | inactive transposase YbfQ/H repeat‑associated putative transposase YbfD |
| RA | 749,898 | G→A | R758C (CGC→TGC) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,015,757 | Δ1 bp | coding (43/168 nt) | rmf → | ribosome modulation factor |
| JC JC | 1,091,173 | IS5 (+) +4 bp | coding (1114‑1117/2424 nt) | pgaA ← | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export outer membrane porin |
| JC JC | 1,103,637 | IS5 (+) +4 bp | intergenic (‑441/‑311) | csgD ← / → csgB | DNA‑binding transcriptional dual regulator CsgD/curlin, minor subunit |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,136,605 | G→A | G111E (GGA→GAA) | flgI → | flagellar P‑ring protein |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| JC JC | 1,303,314 | IS186 (–) +6 bp :: Δ1 bp | coding (416‑421/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,322,868 | G→A | Q27* (CAG→TAG) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,345,203 | Δ1 bp | coding (1540/1986 nt) | pdeR ← | cyclic di‑GMP phosphodiesterase PdeR |
| RA | 1,395,042 | G→A | T294I (ACC→ATC) | ynaI ← | small conductance mechanosensitive channel YnaI |
| MC JC | 1,397,239 | Δ28,738 bp | IS5‑mediated | ynaJ–[ydaY] | 41 genes ynaJ, uspE, fnr, ogt, abgT, abgB, abgA, abgR, mcaS, smrA, dgcM, ynaN, zntB, fnrS, ynaL, dbpA, ttcA, intR, xisR, rcbA, ralA, ralR, recT, recE, racC, ydaE, kilR, kilS, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzoR, trkG, ynaK, [ydaY] |
| RA | 1,626,727 | C→A | L218L (CTG→CTT) | dcp ← | peptidyl‑dipeptidase Dcp |
| RA | 1,641,438 | A→G | N39N (AAT→AAC) | cspB ← | cold shock‑like protein CspB |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,684,504 | G→T | Q82H (CAG→CAT) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,712,661 | A→T | intergenic (+503/‑108) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,895,329 | G→A | Q175Q (CAG→CAA) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,969,375 | C→A | intergenic (‑11/+8) | cheR ← / ← tap | chemotaxis protein methyltransferase/methyl‑accepting chemotaxis protein Tap |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,026,349 | G→A | R557W (CGG→TGG) | dgcQ ← | diguanylate cyclase DgcQ |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,108,470 | C→T | S372N (AGT→AAT) | rfbX ← | polyisoprenol‑linked O16‑antigen repeat unit flippase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,202,345 | T→A | D689E (GAT→GAA) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,278,289 | A→G | intergenic (‑52/+281) | yejG ← / ← bcr | protein YejG/multidrug efflux pump Bcr |
| RA | 2,388,299 | T→C | Q43R (CAA→CGA) | yfbN ← | uncharacterized protein YfbN |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,420,652 | 2 bp→TG | coding (32‑33/648 nt) | yfcG → | disulfide bond oxidoreductase YfcG |
| RA | 2,430,737 | G→A | I9I (ATC→ATT) | cvpA ← | colicin V production protein |
| RA | 2,537,509 | G→A | A56A (GCG→GCA) | yfeK → | DUF5329 domain‑containing protein YfeK |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,577,284 | G→A | S365L (TCA→TTA) | maeB ← | malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+)) |
| RA | 2,680,564 | G→A | P728S (CCG→TCG) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,704,184 | C→T | intergenic (‑121/+151) | rnc ← / ← lepB | RNase III/signal peptidase I |
| RA | 2,739,388 | C→A | E228* (GAG→TAG) | tyrA ← | fused chorismate mutase/prephenate dehydrogenase |
| JC JC | 2,765,062 | IS2 (–) +5 bp | coding (88‑92/1617 nt) | abpA ← | anti‑bacteriophage protein |
| RA | 2,789,030 | C→T | Q16* (CAG→TAG) | glaH → | glutarate dioxygenase GlaH |
| RA | 2,864,262 | C→T | S9S (TCC→TCT) | ygbM → | putative 2‑oxo‑tetronate isomerase YgbM |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,870,068 | G→A | T69T (ACC→ACT) | umpG ← | broad specificity 5'(3')‑nucleotidase and polyphosphatase |
| RA | 2,900,293 | 2 bp→CT | intergenic (‑20/‑298) | ygcW ← / → yqcE | putative deoxygluconate dehydrogenase/putative transport protein YqcE |
| RA | 2,966,382 | C→T | G685R (GGG→AGG) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,156,738 | A→T | E39V (GAA→GTA) | dkgA → | methylglyoxal reductase DkgA |
| RA | 3,160,398 | G→A | P250L (CCA→CTA) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,166,817 | G→A | P301L (CCG→CTG) | ygiS ← | putative deoxycholate binding periplasmic protein |
| MC JC | 3,305,134 | Δ19 bp | coding (666‑684/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,352,260 | G→A | R256C (CGT→TGT) | arcB ← | sensor histidine kinase ArcB |
| JC JC | 3,367,195 | IS2 (+) +5 bp | coding (270‑274/717 nt) | yhcF → | DUF1120 domain‑containing protein YhcF |
| JC JC | 3,485,077 | IS2 (–) +5 bp | coding (588‑592/870 nt) | prkB → | putative phosphoribulokinase |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,632,121 | C→T | W157* (TGG→TAG) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| MC JC | 3,653,231 | Δ63,334 bp | IS5‑mediated | yhiS–[yiaD] | 52 genes yhiS, slp, dctR, yhiD, hdeB, hdeA, hdeD, arrS, gadE, gadF, mdtE, mdtF, gadW, gadY, gadX, gadA, ccp, treF, yhjB, rcdB, yhjD, yhjE, yhjG, pdeH, kdgK, yhjJ, dctA, pdeK, bcsC, bcsZ, bcsB, bcsA, yhjR, bcsE, bcsF, bcsG, ldrD, rdlD, yhjV, dppF, dppD, dppC, dppB, dppA, proK, eptB, yhjX, yhjY, tag, yiaC, bisC, [yiaD] |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,900,993 | C→T | D410N (GAT→AAT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 4,001,322 | T→A | intergenic (+48/‑104) | ysgD → / → corA | protein YsgD/Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| JC JC | 4,002,526 | IS5 (–) +4 bp | coding (271‑274/381 nt) | yigF ← | DUF2628 domain‑containing protein YigF |
| RA | 4,026,734 | Δ1 bp | coding (208/702 nt) | fre → | NAD(P)H‑flavin reductase |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,152,733 | G→A | I122I (ATC→ATT) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,360,480 | G→A | T485T (ACC→ACT) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,372,088 | A→G | E355G (GAA→GGA) | groL → | chaperonin GroEL |
| RA | 4,561,138 | T→C | F70S (TTT→TCT) | kptA → | RNA 2'‑phosphotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196265 | 1211460 | 15196 | 33 [31] | [24] 33 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 117 [0] | [0] 104 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423884–3424233 | 3424482–3424239 | 7–599 | 32 [30] | [29] 32 | rrlD | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 60 (0.630) | 44/598 | 0.9 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 116 (1.210) | 78/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 104 (1.080) | 73/598 | 0.1 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||