mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 3,011 | C→T | 19.4% | R71C (CGT→TGT) | thrB → | homoserine kinase |
| RA | 76,805 | T→A | 100% | E165D (GAA→GAT) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 87,481 | C→A | 100% | T42K (ACA→AAA) | ilvH → | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit |
| RA | 125,085 | Δ1 bp | 100% | coding (2069/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 710,595 | G→T | 100% | P18T (CCT→ACT) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| 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 | 1,441,833 | G→C | 5.3% | intergenic (‑90/+21) | hslJ ← / ← ldhA | lipoprotein implicated in Novobiocin resistance/D‑lactate dehydrogenase |
| RA | 1,441,835 | A→T | 5.6% | intergenic (‑92/+19) | hslJ ← / ← ldhA | lipoprotein implicated in Novobiocin resistance/D‑lactate dehydrogenase |
| RA | 1,466,639 | C→T | 5.6% | pseudogene (1248/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| 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 | 2,416,622 | C→G | 100% | Q626E (CAG→GAG) | pta → | phosphate acetyltransferase |
| RA | 2,656,412 | C→T | 21.1% | intergenic (‑54/+124) | pepB ← / ← iscX | aminopeptidase B/accessory iron‑sulfur cluster assembly protein IscX |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,176,209 | C→A | 100% | D209Y (GAT→TAT) | cpdA ← | cAMP phosphodiesterase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,774,207 | C→T | 6.0% | intergenic (+13/‑217) | mtlA → / → mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,774,214 | C→T | 6.8% | intergenic (+20/‑210) | mtlA → / → mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,774,215 | A→G | 8.2% | intergenic (+21/‑209) | mtlA → / → mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,833,354 | C→T | 11.2% | C395Y (TGC→TAC) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 3,839,567 | G→C | 10.9% | L143V (CTT→GTT) | nlpA ← | lipoprotein‑28 |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,082,696 | G→C | 6.6% | Q22E (CAG→GAG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | 4,159,068 | G→A | 30.8% | M193I (ATG→ATA) | oxyR → | DNA‑binding transcriptional dual regulator OxyR |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,207,576 | A→G | 12.4% | intergenic (‑44/‑571) | purH ← / → rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| RA | 4,296,060 | C→T | 34.8% | 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 | 4,472,434 | G→A | 8.0% | R34* (CGA→TGA) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,472,437 | T→C | 9.3% | N33D (AAT→GAT) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,488,331 | C→G | 7.6% | I338M (ATC→ATG) | lptG → | lipopolysaccharide transport system protein LptG |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 366238 | 366402 | 165 | 5 [4] | [4] 5 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913 | 1196288 | 1211429 | 15142 | 5 [4] | [4] 5 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423667–3424234 | 3424516–3424238 | 5–850 | 5 [4] | [4] 5 | rrfD–[rrlD] | rrfD,[rrlD] |
| * | * | ÷ | NC_000913 | 3621187–3622297 | 3653132–3652031 | 29735–31946 | 5 [4] | [4] 5 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3424418 = | NA (NA) | 5 (0.220) | 5/256 | NT | 100% | noncoding (2366/2904 nt) | rrlD | 23S ribosomal RNA |
| ? | NC_000913 | = 3946053 | 0 (0.000) | noncoding (2350/2904 nt) | rrlC | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3776001 = | 35 (1.470) | 3 (0.140) | 3/246 | NT | 8.7% | coding (430/588 nt) | mtlR | transcriptional repressor MtlR |
| ? | NC_000913 | 3776026 = | 30 (1.360) | coding (455/588 nt) | mtlR | transcriptional repressor MtlR | |||||
| * | ? | NC_000913 | 3855060 = | 37 (1.560) | 4 (0.180) | 4/250 | NT | 9.9% | coding (1139/1185 nt) | emrD | multidrug efflux pump EmrD |
| ? | NC_000913 | 3855100 = | 38 (1.690) | coding (1179/1185 nt) | emrD | multidrug efflux pump EmrD | |||||