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 | 120,044 | C→A | T255K (ACG→AAG) | ampE → | protein AmpE |
| RA | 120,080 | C→T | S267L (TCG→TTG) | ampE → | protein AmpE |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 270,288 | G→A | pseudogene (11/263 nt) | insN → | IS911A regulator fragment |
| RA | 430,095 | 2 bp→AT | coding (591‑592/972 nt) | secF → | Sec translocon accessory complex subunit SecF |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 559,967 | G→A | E91K (GAA→AAA) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 637,183 | G→A | H146Y (CAC→TAC) | ybdO ← | putative LysR family DNA‑binding transcriptional regulator YbdO |
| JC JC | 789,869 | IS2 (+) +5 bp | coding (107‑111/1149 nt) | galK ← | galactokinase |
| RA | 1,044,792 | C→T | D338N (GAC→AAC) | gfcE ← | putative exopolysaccharide export lipoprotein GfcE |
| RA | 1,072,982 | C→A | E344* (GAA→TAA) | rutA ← | pyrimidine monooxygenase RutA |
| JC JC | 1,105,495 | IS1 (–) +9 bp | coding (82‑90/312 nt) | ymdA → | uncharacterized protein YmdA |
| JC JC | 1,222,261 | IS5 (–) +4 bp | intergenic (+3060/+41) | ymgF → / ← ymgD | inner membrane protein YmgF/PF16456 family protein YmgD |
| RA | 1,292,173 | Δ1 bp | coding (717/909 nt) | galU → | UTP‑‑glucose‑1‑phosphate uridylyltransferase |
| JC | 1,301,555 | Δ11 bp | coding (374‑384/1632 nt) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,304,579 | 4 bp→TCAA | coding (746‑749/909 nt) | oppC → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppC |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,340,616 | G→A | G20D (GGC→GAC) | lapB → | lipopolysaccharide assembly protein B |
| JC JC | 1,590,490 | IS2 (+) +5 bp | intergenic (‑489/+360) | ydeT ← / ← hipA | fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,909,372 | IS2 (+) +5 bp | coding (724‑728/792 nt) | kdgR ← | DNA‑binding transcriptional repressor KdgR |
| MC JC | 2,102,944 | Δ7,292 bp | IS5‑mediated | [wbbL]–[rfbA] | [wbbL], wbbK, wbbJ, wbbI, wbbH, glf, rfbX, rfbC, [rfbA] |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,238,667 | IS1 (–) +9 bp | coding (615‑623/1521 nt) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| JC JC | 2,317,303 | IS2 (–) +5 bp | coding (2570‑2574/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,320,955 | C→T | Q305* (CAG→TAG) | atoS → | sensor histidine kinase AtoS |
| JC JC | 2,482,241 | IS5 (+) +4 bp | coding (1096‑1099/1164 nt) | emrK ← | tripartite efflux pump membrane fusion protein EmrK |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,107,665 | G→T | A497A (GCC→GCA) | speC ← | constitutive ornithine decarboxylase |
| RA | 3,111,082 | T→C | E15E (GAA→GAG) | yghD ← | putative type II secretion system M‑type protein YghD |
| RA | 3,188,716 | T→C | pseudogene (1285/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,441,432 | G→A | L82L (CTG→TTG) | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,463,939 | 2 bp→AA | coding (18‑19/1164 nt) | gspL → | Type II secretion system protein GspL |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,520,108 | 2 bp→TT | coding (595‑596/1239 nt) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,682,537 | C→T | G304D (GGC→GAC) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,732,723 | G→A | E175K (GAG→AAG) | xylG → | xylose ABC transporter ATP binding subunit |
| MC JC | 3,890,570 | Δ8 bp | coding (335‑342/1248 nt) | tnaB → | tryptophan:H(+) symporter TnaB |
| RA | 4,013,144 | C→T | S31F (TCC→TTC) | metE → | cobalamin‑independent homocysteine transmethylase |
| RA | 4,121,437 | G→A | T104I (ACC→ATC) | hslU ← | ATPase component of the HslVU protease |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,448,888 | C→T | P66L (CCT→CTT) | chpB → | endoribonuclease toxin ChpB |
| RA | 4,465,767 | C→T | L138L (TTG→TTA) | treB ← | trehalose‑specific PTS enzyme IIBC component |
| RA | 4,466,656 | G→A | A197A (GCC→GCT) | treR ← | DNA‑binding transcriptional repressor TreR |
| RA | 4,492,685 | C→T | E223K (GAA→AAA) | idnO ← | 5‑keto‑D‑gluconate 5‑reductase |
| RA | 4,592,206 | G→A | D184N (GAT→AAT) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 108 [0] | [0] 138 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423813–3424486 | 3424486 | 1–674 | 35 [34] | [34] 38 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 273955 = | NA (NA) | 67 (0.690) | 54/598 | 0.6 | 63.2% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 536884 = | 39 (0.400) | coding (299/879 nt) | glxR | tartronate semialdehyde reductase 2 | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 71 (0.730) | 59/596 | 0.4 | 64.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 536887 | 39 (0.400) | coding (302/879 nt) | glxR | tartronate semialdehyde reductase 2 | |||||
| * | ? | NC_000913 | 1207790 = | 21 (0.210) | 75 (0.810) | 57/566 | 0.4 | 77.8% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 23 (0.250) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.240) | 71 (0.770) | 54/566 | 0.5 | 76.0% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 23 (0.250) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 123 (1.280) | 71/590 | 0.1 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 107 (1.090) | 67/598 | 0.2 | 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) | 138 (1.410) | 95/598 | 0.0 | 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 | |||||
| * | ? | NC_000913 | 4542682 = | 128 (1.310) | 32 (0.340) | 25/580 | 3.0 | 21.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 110 (1.160) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 133 (1.360) | 35 (0.370) | 29/580 | 2.4 | 22.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 110 (1.160) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||