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 | 147,213 | 2 bp→TT | coding (246‑247/903 nt) | rpnC → | recombination‑promoting nuclease RpnC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 299,490 | T→C | E482G (GAA→GGA) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 364,170 | 2 bp→AA | coding (2135‑2136/3075 nt) | lacZ ← | beta‑galactosidase |
| RA | 447,538 | A→G | F56F (TTT→TTC) | cyoE ← | heme O synthase |
| RA | 460,060 | C→T | I391I (ATC→ATT) | lon → | Lon protease |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 579,502 | A→G | N31N (AAT→AAC) | ybcV ← | DUF1398 domain‑containing protein YbcV |
| RA | 579,540 | T→C | N19D (AAC→GAC) | ybcV ← | DUF1398 domain‑containing protein YbcV |
| RA | 579,651 | C→T | intergenic (‑57/‑229) | ybcV ← / → ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| RA | 579,671 | T→C | intergenic (‑77/‑209) | ybcV ← / → ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| RA | 584,506 | C→T | intergenic (+76/+174) | appY → / ← ompT | DNA‑binding transcriptional activator AppY/omptin family outer membrane protease OmpT |
| JC JC | 585,707 | IS2 (+) +5 bp | intergenic (‑74/+436) | ompT ← / ← envY | omptin family outer membrane protease OmpT/DNA‑binding transcriptional activator EnvY |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| JC JC | 698,995 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | coding (178‑183/1665 nt) | asnB ← | asparagine synthetase B |
| RA | 789,580 | C→A | E134* (GAA→TAA) | galK ← | galactokinase |
| RA | 882,583 | A→C | L51W (TTG→TGG) | deoR ← | DNA‑binding transcriptional repressor DeoR |
| RA | 928,622 | G→A | L192L (CTG→TTG) | cydC ← | glutathione/L‑cysteine ABC exporter subunit CydC |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| JC JC | 1,226,985 | IS2 (+) +5 bp | intergenic (+17/+82) | ycgJ → / ← pliG | PF05666 family protein YcgJ/inhibitor of g‑type lysozyme |
| JC JC | 1,303,274 | IS150 (+) +3 bp | coding (376‑378/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,477,804 | C→T | L62F (CTT→TTT) | ynbA → | CDP‑alcohol phosphatidyltransferase domain‑containing protein YnbA |
| JC JC | 1,495,083 | IS2 (+) +5 bp | intergenic (‑12/‑201) | ydcI ← / → ydcJ | DNA‑binding transcriptional dual regulator YdcI/DUF1338 domain‑containing protein YdcJ |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,869,314 | G→A | S120S (TCG→TCA) | yeaH → | DUF444 domain‑containing protein YeaH |
| RA | 1,887,023 | G→A | I323I (ATC→ATT) | rnd ← | RNase D |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,039,555 | A→G | L26L (TTA→TTG) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,061,989 | T→C | intergenic (‑56/‑271) | nac ← / → asnV | DNA‑binding transcriptional dual regulator Nac/tRNA‑Asn |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,317,225 | IS2 (–) +5 bp | coding (2648‑2652/2850 nt) | rcsC ← | histidine kinase RcsC |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| JC JC | 2,464,157 | IS5 (–) +4 bp | intergenic (+87/+92) | yfdF → / ← mlaA | protein YfdF/intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA |
| RA | 2,474,885 | G→C | intergenic (+29/‑99) | yfdQ → / → yfdR | DUF2303 domain‑containing protein YfdQ/5'‑deoxynucleotidase |
| RA | 2,513,749 | C→G | F236L (TTC→TTG) | nupC → | nucleoside:H(+) symporter NupC |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,780,701 | T→C | N676D (AAT→GAT) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,866,959 | A→C | I198S (ATC→AGC) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,036,781 | G→A | F442F (TTC→TTT) | recJ ← | ssDNA‑specific exonuclease RecJ |
| JC JC | 3,252,952 | IS2 (–) +5 bp | coding (42‑46/357 nt) | yhaI → | putative inner membrane protein |
| RA | 3,413,827 | G→A | intergenic (‑362/‑37) | envR ← / → acrE | DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE |
| RA | 3,474,290 | T→C | K88R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| 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 | 3,572,319 | T→G | E395A (GAA→GCA) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,599,379 | T→G | K94Q (AAA→CAA) | livJ ← | branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein |
| RA | 3,633,668 | T→A | intergenic (‑1078/‑1173) | yhiJ ← / → yhiM | DUF4049 domain‑containing protein YhiJ/inner membrane protein YhiM |
| JC JC | 3,725,990 | IS5 (–) +4 bp | coding (104‑107/996 nt) | wecH → | O‑acetyltransferase WecH |
| RA | 3,765,752 | C→G | R1190R (CGC→CGG) | rhsA → | rhs element protein RhsA |
| RA | 3,765,830 | G→A | R1216R (CGG→CGA) | rhsA → | rhs element protein RhsA |
| RA | 3,765,854 | G→A | G1224G (GGG→GGA) | rhsA → | rhs element protein RhsA |
| RA | 4,018,586 | G→A | L418L (CTG→CTA) | rmuC → | putative recombination limiting protein RmuC |
| RA | 4,124,345 | G→A | Q38* (CAG→TAG) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,216,329 | C→T | I284I (ATC→ATT) | aceB → | malate synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,309,712 | C→T | W423* (TGG→TGA) | alsA ← | D‑allose ABC transporter ATP binding subunit |
| RA | 4,311,002 | 2 bp→GT | intergenic (‑22/+104) | alsA ← / ← alsB | D‑allose ABC transporter ATP binding subunit/D‑allose ABC transporter periplasmic binding protein |
| RA | 4,578,759 | G→A | I193I (ATC→ATT) I193I (ATC→ATT) |
mcrB ← mcrB ← |
5‑methylcytosine‑specific restriction enzyme subunit McrB 5‑methylcytosine‑specific restriction enzyme subunit McrB |
| RA | 4,624,587 | G→A | S68L (TCA→TTA) | ytjB ← | putative inner membrane protein Smp |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 480924 | 481029 | 106 | 31 [3] | [0] 21 | tomB/acrB | Hha toxicity modulator TomB/multidrug efflux pump RND permease AcrB |
| * | * | ÷ | NC_000913 | 807310 | 807447 | 138 | 6 [5] | [5] 6 | [ybhB] | [ybhB] |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978507 | 13–776 | 34 [0] | [0] 25 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2726303–2729240 | 2730725–2729570 | 331–4423 | 6 [5] | [5] 6 | [rrlG]–[rrsG] | [rrlG],gltW,[rrsG] |
| * | * | ÷ | NC_000913 | 3764305–3765289 | 3765692 | 404–1388 | 6 [5] | [4] 6 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 21 (0.580) | 21/488 | 0.7 | 100% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 481030 = | 0 (0.000) | intergenic (‑322/+224) | tomB/acrB | Hha toxicity modulator TomB/multidrug efflux pump RND permease AcrB | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 28 (0.770) | 25/488 | 0.4 | 90.3% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 480923 | 3 (0.080) | intergenic (‑215/+331) | tomB/acrB | Hha toxicity modulator TomB/multidrug efflux pump RND permease AcrB | |||||
| * | ? | NC_000913 | = 566774 | 45 (1.240) | 36 (1.000) | 20/484 | 0.7 | 45.7% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 41 (1.130) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 676343 = | 15 (0.420) | 79 (2.190) | 67/484 | 0.0 | 84.0% | coding (205/978 nt) | ybeQ | Sel1 repeat‑containing protein YbeQ |
| ? | NC_000913 | = 689045 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 17 (0.470) | 9 (0.260) | 8/456 | 2.1 | 36.8% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 15 (0.440) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 17 (0.470) | 9 (0.260) | 8/456 | 2.1 | 36.8% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 15 (0.440) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 44 (1.230) | 43/480 | 0.0 | 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) | 32 (0.880) | 30/488 | 0.3 | 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) | 25 (0.690) | 25/488 | 0.4 | 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 | |||||