mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 83,587 | A→C | 21.3% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 21.2% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 124,241 | C→T | 100% | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 460,772 | T→G | 100% | S629A (TCG→GCG) | lon → | Lon protease |
| RA | 754,446 | A→G | 100% | L8P (CTC→CCC) | gltA ← | citrate synthase |
| RA | 760,485 | G→A | 100% | G594S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 861,069 | C→T | 17.4% | R513H (CGC→CAC) | ybiW ← | putative pyruvate formate lyase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,371,456 | G→C | 22.2% | S414T (AGT→ACT) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,852,271 | C→T | 46.5% | R129W (CGG→TGG) ‡ | pncA → | nicotinamidase |
| RA | 1,852,273 | G→C | 43.7% | R129R (CGG→CGC) ‡ | pncA → | nicotinamidase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,368,101 | T→C | 100% | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,661,821 | C→G | 100% | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,310,841 | C→T | 40.9% | E110K (GAA→AAA) | pnp ← | polynucleotide phosphorylase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,204 | G→A | 53.8% | intergenic (‑105/+128) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,202,409 | C→T | 23.7% | H162Y (CAC→TAC) | zraS → | sensory histidine kinase ZraS |
| RA | 4,296,060 | C→T | 29.4% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423783–3424233 | 3424520–3424241 | 9–738 | 3 [2] | [2] 3 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315290 | 12 (0.740) | 4 (0.330) +34 bp |
3/196 | NT | 26.5% | noncoding (62/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 18 (1.110) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 913 (56.590) | 224/262 | NT | 98.1% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 18 (1.110) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 608008 = | NA (NA) | 22 (1.380) | 19/258 | NT | 61.1% | noncoding (2/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 839235 | 14 (0.880) | intergenic (‑28/+14) | ybiX/fiu | PKHD‑type hydroxylase YbiX/putative iron siderophore outer membrane transporter | |||||
| * | ? | NC_000913 | = 609349 | NA (NA) | 17 (1.060) | 15/260 | NT | 51.5% | noncoding (1343/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 830157 = | 16 (1.000) | coding (487/672 nt) | cecR | DNA‑binding transcriptional dual regulator CecR | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.430) | 11 (0.770) | 11/232 | NT | 60.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 8 (0.560) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 8 (0.490) | 7 (0.490) | 7/232 | NT | 48.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 8 (0.560) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1418580 = | 13 (0.800) | 3 (0.190) | 3/252 | NT | 18.5% | intergenic (‑351/‑91) | kilR/sieB | Rac prophage; inhibitor of FtsZ, killing protein/Rac prophage; phage superinfection exclusion protein |
| ? | NC_000913 | 1418602 = | 14 (0.900) | intergenic (‑373/‑69) | kilR/sieB | Rac prophage; inhibitor of FtsZ, killing protein/Rac prophage; phage superinfection exclusion protein | |||||
| * | ? | NC_000913 | = 4171803 | 19 (1.170) | 4 (0.250) | 3/260 | NT | 19.2% | intergenic (+47/‑254) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase |
| ? | NC_000913 | = 4213162 | 15 (0.940) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA/stress response protein | |||||