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 | 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 | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| 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 | 940,751 | T→C | 10.0% | intergenic (+31/‑208) | serS → / → dmsA | serine‑‑tRNA ligase/dimethyl sulfoxide reductase subunit A |
| RA | 940,754 | G→A | 10.5% | intergenic (+34/‑205) | serS → / → dmsA | serine‑‑tRNA ligase/dimethyl sulfoxide reductase subunit A |
| RA | 1,074,945 | T→G | 18.1% | N1313T (AAC→ACC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,285,190 | T→A | 13.4% | L18I (TTA→ATA) | narJ → | nitrate reductase 1 molybdenum cofactor assembly chaperone |
| 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 | 1,572,964 | C→T | 12.1% | A747T (GCA→ACA) | pqqL ← | putative zinc peptidase |
| RA | 1,666,468 | A→T | 14.2% | Q385L (CAG→CTG) | clcB → | putative chloride:H(+) antiporter ClcB |
| 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 | 1,985,112 | C→G | 17.4% | intergenic (‑43/+27) | araG ← / ← araF | arabinose ABC transporter ATP binding subunit/arabinose ABC transporter periplasmic binding protein |
| 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 | 2,716,030 | T→G | 16.0% | intergenic (+20/+36) | eamB → / ← grcA | cysteine/O‑acetylserine exporter EamB/stress‑induced alternate pyruvate formate‑lyase subunit |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,072,800 | C→T | 11.1% | D298N (GAT→AAT) | epd ← | D‑erythrose‑4‑phosphate dehydrogenase |
| RA | 3,072,802 | A→T | 11.5% | V297D (GTC→GAC) | epd ← | D‑erythrose‑4‑phosphate dehydrogenase |
| RA | 3,441,060 | T→C | 14.9% | K206E (AAG→GAG) | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,441,061 | G→C | 14.4% | S205S (TCC→TCG) ‡ | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,441,062 | G→A | 14.6% | S205F (TCC→TTC) ‡ | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,733,502 | G→A | 12.7% | R434R (AGG→AGA) | xylG → | xylose ABC transporter ATP binding subunit |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,094,581 | A→G | 13.6% | intergenic (‑309/+142) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,236,011 | T→C | 18.2% | S36P (TCG→CCG) | yjbE → | uncharacterized protein YjbE |
| RA | 4,296,060 | C→T | 37.0% | 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 |
| RA | 4,365,452 | G→T | 12.0% | intergenic (‑96/+20) | cutA ← / ← dcuA | copper binding protein CutA/C4‑dicarboxylate transporter DcuA |
| RA | 4,365,453 | A→C | 12.1% | intergenic (‑97/+19) | cutA ← / ← dcuA | copper binding protein CutA/C4‑dicarboxylate transporter DcuA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2066278–2066604 | 2066604 | 1–327 | 9 [8] | [7] 9 | [insH‑6] | [insH‑6] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315646 | NA (NA) | 4 (0.150) | 4/254 | NT | NA | noncoding (418/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315665 | NA (NA) | noncoding (437/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1027 (37.840) | 232/262 | NT | 97.4% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 28 (1.020) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 1202235 | 26 (0.950) | 3 (0.120) | 3/250 | NT | 10.6% | intergenic (‑151/+24) | ymfJ/ymfK | e14 prophage; protein YmfJ/e14 prophage; putative repressor protein YmfK |
| ? | NC_000913 | = 1202239 | 26 (1.000) | intergenic (‑155/+20) | ymfJ/ymfK | e14 prophage; protein YmfJ/e14 prophage; putative repressor protein YmfK | |||||
| * | ? | NC_000913 | 1207790 = | 20 (0.730) | 7 (0.290) | 7/232 | NT | 29.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 16 (0.670) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 21 (0.770) | 4 (0.170) | 4/232 | NT | 18.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 16 (0.670) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 2252869 | NA (NA) | 4 (0.150) | 3/250 | NT | NA | noncoding (19/28 nt) | other | REPv157b |
| ? | NC_000913 | = 2252879 | NA (NA) | noncoding (9/28 nt) | other | REPv157b | |||||
| * | ? | NC_000913 | 2727891 = | NA (NA) | 4 (0.150) | 4/252 | NT | NA | noncoding (1294/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA | |||||