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 | 16,923 | T→G | 9.7% | K13T (AAG→ACG) | mokC ← | regulatory protein MokC |
| RA | 95,730 | A→G | 32.4% | M361V (ATG→GTG) | murF → | D‑alanyl‑D‑alanine‑adding enzyme |
| 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 | 753,346 | T→G | 63.8% | I375L (ATT→CTT) | gltA ← | citrate synthase |
| RA | 756,792 | G→T | 100% | E296* (GAA→TAA) | sdhA → | succinate:quinone oxidoreductase, FAD binding protein |
| RA | 782,999 | T→G | 7.3% | L305L (CTT→CTG) | nadA → | quinolinate synthase |
| RA | 783,000 | C→A | 7.5% | Q306K (CAG→AAG) | nadA → | quinolinate synthase |
| RA | 887,468 | G→A | 7.4% | A16T (GCC→ACC) | rcdA → | DNA‑binding transcriptional regulator RcdA |
| RA | 915,080 | G→C | 6.9% | intergenic (‑223/+272) | lysO ← / ← aqpZ | L‑lysine exporter/water channel AqpZ |
| 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 | 1,371,967 | G→A | 9.5% | G20D (GGC→GAC) | ycjN → | putative ABC transporter periplasmic binding protein YcjN |
| RA | 1,466,201 | T→C | 6.3% | pseudogene (810/2518 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 | 2,187,313 | T→C | 12.6% | intergenic (+15/+67) | rcnB → / ← yehA | periplasmic protein involved in nickel/cobalt export/putative fimbrial adhesin YehA |
| RA | 2,489,152 | C→T | 100% | S6N (AGC→AAC) | yfdE ← | acetyl‑CoA:oxalate CoA‑transferase |
| RA | 2,562,169 | C→T | 7.9% | P20L (CCG→CTG) | yffO → | CPZ‑55 prophage; uncharacterized protein YffO |
| RA | 2,661,793 | C→A | 100% | L113F (TTG→TTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,333,767 | G→A | 6.7% | A20T (GCA→ACA) | ispB → | all‑trans‑octaprenyl‑diphosphate synthase |
| RA | 3,389,186 | T→C | 100% | N51S (AAC→AGC) | aaeX ← | DUF1656 domain‑containing protein AaeX |
| 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] | |
| RA | 3,954,274 | A→C | 5.1% | E266A (GAA→GCA) | ilvD → | dihydroxy‑acid dehydratase |
| RA | 3,959,515 | T→A | 6.8% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase (NADP(+))/peptidyl‑prolyl cis‑trans isomerase C |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| JC | 4,158,922 | Δ6 bp | 100% | coding (433‑438/918 nt) | oxyR → | DNA‑binding transcriptional dual regulator OxyR |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,287,423:1 | +T | 100% | intergenic (‑52/‑341) | acs ← / → nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| RA | 4,295,929 | T→C | 6.3% | intergenic (+135/+507) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,060 | C→T | 30.4% | 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 |
| RA | 4,335,655 | T→A | 5.0% | intergenic (‑65/+39) | eptA ← / ← adiC | phosphoethanolamine transferase EptA/arginine:agmatine antiporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196269 | 1211454 | 15186 | 16 [15] | [14] 16 | [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 | 3621201–3622297 | 3653121–3652031 | 29735–31921 | 16 [13] | [14] 16 | [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 | 3774236 = | NA (NA) | 3 (0.060) | 3/250 | NT | NA | intergenic (+42/‑188) | mtlA/mtlD | mannitol‑specific PTS enzyme IICBA component/mannitol‑1‑phosphate 5‑dehydrogenase |
| ? | NC_000913 | 3774261 = | NA (NA) | noncoding (25/29 nt) | other | REPv271a | |||||
| * | ? | NC_000913 | = 4143957 | 50 (0.990) | 3 (0.060) | 3/254 | NT | 5.7% | intergenic (+13/‑38) | frwB/pflD | putative PTS enzyme IIB component FrwB/putative formate acetyltransferase 2 |
| ? | NC_000913 | = 4143965 | 52 (1.070) | intergenic (+21/‑30) | frwB/pflD | putative PTS enzyme IIB component FrwB/putative formate acetyltransferase 2 | |||||
| * | ? | NC_000913 | 4240158 = | NA (NA) | 3 (0.060) | 3/250 | NT | NA | noncoding (1/37 nt) | other | REP314 |
| ? | NC_000913 | 4240189 = | NA (NA) | noncoding (32/37 nt) | other | REP314 | |||||
| * | ? | NC_000913 | 4295835 = | NA (NA) | 5 (0.100) +GTTGAT |
4/252 | NT | NA | intergenic (+41/+601) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | 4296251 = | NA (NA) | noncoding (31/34 nt) | other | REP321h | |||||
| * | ? | NC_000913 | 4532946 = | 56 (1.110) | 3 (0.060) | 3/252 | NT | 5.6% | coding (238/747 nt) | yjhP | KpLE2 phage‑like element; putative methyltransferase YjhP |
| ? | NC_000913 | 4532970 = | 48 (0.990) | coding (214/747 nt) | yjhP | KpLE2 phage‑like element; putative methyltransferase YjhP | |||||