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 |
| 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 | 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 |
| JC JC | 998,256 | IS3 (–) +4 bp | coding (389‑392/540 nt) | elfA → | putative laminin‑binding fimbrial subunit |
| RA | 1,097,494 | T→A | intergenic (+665/+71) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| 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 | 1,301,992 | 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 | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| RA | 1,922,115 | G→T | intergenic (+99/‑6) | yebV → / → yebW | DUF1480 domain‑containing protein YebV/DUF1482 domain‑containing protein YebW |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC | 2,173,675 | (ATTCGGTTAACGCCTGG)1→2 | intergenic (‑802/+607) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| JC | 2,406,557 | (TGCGGCAGC)1→2 | coding (85/939 nt) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,778,018 | C→T | intergenic (+236/+128) | ypjF → / ← ypjA | toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 2,779,776 | G→A | S984L (TCG→TTG) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,195,419 | T→G | E445D (GAA→GAC) | hldE ← | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase |
| JC JC | 3,350,539 | IS1 (+) +9 bp | intergenic (‑80/‑30) | elbB ← / → arcZ | low activity glyoxalase ElbB/small regulatory RNA ArcZ |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,888,443 | C→A | I3I (ATC→ATA) | tnaC → | tnaAB operon leader peptide |
| RA | 3,906,751 | T→C | intergenic (‑184/+102) | bglG ← / ← phoU | transcriptional antiterminator BglG/negative regulator of the pho regulon |
| 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 |
| JC JC | 4,476,959 | IS5 (+) +4 bp | coding (1523‑1526/1815 nt) | yjgL → | protein YjgL |
| 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 | 1978503–1979269 | 1979336 | 68–834 | 118 [1] | [0] 95 | insB5–insA5 | insB5,insA5 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 44 (0.420) | 53 (0.530) | 45/566 | 1.0 | 54.5% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 47 (0.470) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 44 (0.420) | 57 (0.570) | 44/566 | 1.1 | 56.3% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 47 (0.470) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 105 (1.040) | 75/574 | 0.1 | 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) | 125 (1.240) | 84/574 | 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 | = 1978502 | 1 (0.010) | 101 (1.210) +62 bp |
60/474 | 0.1 | 99.2% | intergenic (‑305/+16) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| ? | NC_000913 | = 2102943 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979337 = | 0 (0.000) | 94 (0.890) | 68/598 | 0.3 | 100% | intergenic (‑122/‑416) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 37 (0.350) | 31/598 | 2.5 | 21.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3321591 | 134 (1.270) | coding (23/1626 nt) | yhbX | putative hydrolase YhbX | |||||
| * | ? | NC_000913 | 3321588 = | 130 (1.230) | 42 (0.400) | 34/598 | 2.2 | 24.4% | coding (26/1626 nt) | yhbX | putative hydrolase YhbX |
| ? | NC_000913 | = 3366750 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 77 (0.730) | 61/598 | 0.5 | 67.5% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4536380 = | 37 (0.350) | intergenic (‑2327/‑217) | topAI/ythB | toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/protein YthB | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 77 (0.730) | 53/598 | 0.8 | 67.5% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4536387 | 37 (0.350) | intergenic (‑2334/‑210) | topAI/ythB | toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/protein YthB | |||||