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 | 206,083 | G→A | E320K (GAA→AAA) | dnaE → | DNA polymerase III subunit alpha |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 260,173 | Δ13,782 bp | IS5‑mediated | proB–[ykfC] | 19 genes proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 339,546 | C→T | P408S (CCG→TCG) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 366,997 | 2 bp→TT | coding (513‑514/1083 nt) | lacI ← | DNA‑binding transcriptional repressor LacI |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| RA | 836,451 | C→T | A34V (GCC→GTC) | hcxB → | hydroxycarboxylate dehydrogenase B |
| RA | 1,075,842 | 2 bp→AA | coding (3040‑3041/3963 nt) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,097,494 | T→A | intergenic (+665/+71) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,101,742 | G→A | S129L (TCG→TTG) | csgF ← | curli assembly component CsgF |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,299,498 | +A | intergenic (+253/‑69) | ychE → / → insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,655,288 | G→A | intergenic (‑147/+59) | rspA ← / ← ynfA | mandelate racemase/muconate lactonizing enzyme family protein RspA/putative transporter YnfA |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| RA | 1,811,805 | A→G | K291R (AAG→AGG) | tcyP → | cystine/sulfocysteine:cation symporter |
| RA | 1,812,814 | T→C | K107E (AAA→GAA) | ydjO ← | protein YdjO |
| MC JC | 1,979,271 | Δ101 bp | IS1‑mediated | insA5 ← / → uspC | IS1 family protein InsA/universal stress protein C |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,153,639 | C→T | intergenic (+185/‑7) | sibA → / → sibB | small RNA SibA/small RNA SibB |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,177,240 | A→T | intergenic (‑36/+272) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2/fructose‑bisphosphate aldolase class I |
| RA | 2,406,578 | C→T | V22I (GTT→ATT) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| JC JC | 2,470,639 | IS2 (–) +5 bp | coding (1‑5/147 nt) | yodE ← | toxic protein YodE |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,698,402 | IS30 (–) +2 bp | coding (148‑149/636 nt) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| JC JC | 3,262,484 | +G :: IS5 (–) +3 bp | coding (1175‑1177/1209 nt) | tdcD ← | propionate kinase |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,428,496 | G→A | noncoding (267/1542 nt) | rrsD ← | 16S ribosomal RNA |
| RA | 3,468,728 | C→T | E376K (GAA→AAA) | chiA ← | endochitinase |
| RA | 3,486,415 | C→T | S99L (TCG→TTG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,553,811 | C→G | L243V (CTG→GTG) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,559,852 | C→A | H529N (CAC→AAC) | rtcR → | DNA‑binding transcriptional activator RtcR |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,901 | C→T | intergenic (‑196/+715) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,741,939 | G→A | F198F (TTC→TTT) | plaR ← | DNA‑binding transcriptional repressor PlaR |
| RA | 3,742,697 | G→T | intergenic (‑165/‑36) | plaR ← / → yiaK | DNA‑binding transcriptional repressor PlaR/2,3‑diketo‑L‑gulonate reductase |
| RA | 3,806,341 | C→T | E243K (GAA→AAA) | waaG ← | lipopolysaccharide glucosyltransferase I |
| RA | 3,817,504 | G→A | E277K (GAG→AAG) | yicC → | putative RNase adaptor protein YicC |
| JC JC | 3,890,936 | IS1 (+) +9 bp | coding (701‑709/1248 nt) | tnaB → | tryptophan:H(+) symporter TnaB |
| RA | 4,024,080 | 2 bp→AA | coding (527‑528/783 nt) | tatD → | 3' ‑> 5' ssDNA/RNA exonuclease TatD |
| RA | 4,117,462 | G→A | P210L (CCG→CTG) | glpF ← | glycerol facilitator |
| JC JC | 4,123,637 | IS150 (+) +4 bp | coding (817‑820/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1299499–1300693 | 1300693 | 1–1195 | 116 [0] | [4] 134 | insH21 | insH21 |
| * | * | ÷ | NC_000913 | 3423801–3424234 | 3424486–3424238 | 5–686 | 38 [37] | [37] 38 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4035342–4035730 | 4036918–4035736 | 7–1577 | 38 [37] | [37] 41 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 235428 = | 71 (0.700) | 43 (0.420) | 36/594 | 1.9 | 37.7% | coding (613/723 nt) | yafS | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| ? | NC_000913 | 257908 = | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 235435 | 71 (0.700) | 47 (0.460) | 36/596 | 1.9 | 39.8% | coding (620/723 nt) | yafS | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| ? | NC_000913 | = 258675 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 60 (0.590) | 46/598 | 1.1 | 54.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1561129 = | 51 (0.500) | coding (1353/1551 nt) | ddpA | putative D,D‑dipeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 39 (0.380) | 31/598 | 2.5 | 32.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1844342 = | 82 (0.800) | coding (530/1041 nt) | ynjI | DUF1266 domain‑containing protein YnjI | |||||
| * | ? | NC_000913 | 1207790 = | 34 (0.330) | 87 (0.900) | 64/566 | 0.2 | 74.0% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 29 (0.300) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 35 (0.340) | 85 (0.880) | 61/566 | 0.3 | 73.2% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 29 (0.300) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 113 (1.160) | 70/574 | 0.2 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 130 (1.330) | 85/574 | 0.0 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 106 (1.040) +C |
75/596 | 0.1 | NA | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1300696 | NA (NA) | intergenic (+149/‑486) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1561137 | 51 (0.500) | 44 (0.430) | 35/598 | 2.1 | 46.3% | coding (1345/1551 nt) | ddpA | putative D,D‑dipeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1978503 = | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1844349 | 86 (0.850) | 46 (0.450) | 38/596 | 1.7 | 34.8% | coding (523/1041 nt) | ynjI | DUF1266 domain‑containing protein YnjI |
| ? | NC_000913 | 1978503 = | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 1978501 = | NA (NA) | 80 (1.180) +100 bp |
60/398 | 0.0 | 99.2% | intergenic (‑304/+17) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| ? | NC_000913 | = 1978502 | 1 (0.010) | intergenic (‑305/+16) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||