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 |
| JC | 92,844 | Δ3 bp | 9.6% | coding (1432‑1434/1767 nt) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis; penicillin‑binding protein 3 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,308,013 | Δ1 bp | 5.3% | coding (633/1461 nt) | clsA ← | cardiolipin synthase 1 |
| RA | 1,466,138 | G→A | 7.0% | pseudogene (747/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,201 | T→C | 7.8% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 9.5% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 7.2% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 6.4% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,598,904 | T→C | 55.6% | S436G (AGT→GGT) | lsrK ← | autoinducer‑2 (AI‑2) kinase |
| RA | 1,708,718 | G→A | 6.4% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,930 | C→A | 8.5% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,304,798 | T→C | 12.7% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,316,393 | T→C | 100% | Y73H (TAC→CAC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,316,760 | T→C | 100% | V195A (GTC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,383,800 | G→A | 15.4% | R363Q (CGA→CAA) | elaD → | protease, capable of cleaving an AMC‑ubiquitin model substrate |
| RA | 3,002,095 | C→T | 6.1% | P584L (CCT→CTT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,308,104 | G→A | 87.9% | A274V (GCA→GTA) | nlpI ← | lipoprotein involved in osmotic sensitivity and filamentation |
| MC JC | 3,527,658 | Δ5 bp | 100% | coding (1190‑1194/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,766,527 | C→T | 6.8% | S64F (TCT→TTT) | yibA → | putative immunity protein for polymorphic toxin RhsA; HEAT‑domain protein; lethality reduction protein |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,818,671 | C→G | 6.1% | intergenic (+87/‑203) | dinD → / → yicG | DNA damage‑inducible protein/UPF0126 family inner membrane protein |
| MC JC | 3,992,517 | Δ5 bp | 100% | coding (1365‑1369/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,103,654 | Δ1 bp | 100% | coding (1322/1374 nt) | cpxA ← | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 4,122,731 | A→G | 5.4% | S203S (TCT→TCC) | ftsN ← | essential cell division protein |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 16.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 23.9% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 24.5% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 25.1% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 19.5% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 9.5% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 10.4% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978500 | 1979280 | 781 | 32 [30] | [30] 33 | insB1–insA | insB1,insA |
| * | * | ÷ | NC_000913 | 2533740 | 2536433 | 2694 | 33 [28] | [26] 33 | ptsH–[pdxK] | ptsH,ptsI,crr,[pdxK] |
| * | * | ÷ | NC_000913 | 3423885–3424449 | 3424449 | 1–565 | 32 [29] | [31] 32 | rrlD | 23S ribosomal RNA of rrnD operon |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 33 (0.350) | 33 (0.370) | 30/476 | NT | 50.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 33 (0.370) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 31 (0.330) | 61 (0.690) | 45/476 | NT | 66.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 33 (0.370) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 44 (0.470) | 34/500 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 28 (0.310) | 20/492 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 3220237 = | 87 (0.920) | 6 (0.070) | 3/488 | NT | 5.6% | coding (744/1380 nt) | patA | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent |
| ? | NC_000913 | 3220409 = | 118 (1.300) | coding (916/1380 nt) | patA | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent | |||||
| * | ? | NC_000913 | = 4106253 | 90 (0.960) | 9 (0.100) | 9/508 | NT | 9.1% | coding (434/501 nt) | cpxP | inhibitor of the cpx response; periplasmic adaptor protein |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||