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 | 125,085 | Δ1 bp | 100% | coding (2069/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 192,963 | G→A | 15.0% | R31H (CGT→CAT) | frr → | ribosome‑recycling factor |
| 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 | 756,792 | G→T | 100% | E296* (GAA→TAA) | sdhA → | succinate:quinone oxidoreductase, FAD binding protein |
| 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 | 1,466,201 | T→C | 14.2% | 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 | 2,489,152 | C→T | 100% | S6N (AGC→AAC) | yfdE ← | acetyl‑CoA:oxalate CoA‑transferase |
| RA | 2,579,023 | C→A | 14.1% | Q120K (CAA→AAA) | talA → | transaldolase A |
| RA | 2,661,793 | C→A | 51.4% | L113F (TTG→TTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,661,815 | G→A | 19.6% | T106I (ACC→ATC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| 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 | 3,886,756 | G→A | 5.0% | intergenic (+34/‑72) | yidC → / → mnmE | membrane protein insertase YidC/5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,886,757 | T→C | 5.7% | intergenic (+35/‑71) | yidC → / → mnmE | membrane protein insertase YidC/5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| RA | 3,954,273 | G→T | 8.4% | E266* (GAA→TAA) ‡ | ilvD → | dihydroxy‑acid dehydratase |
| RA | 3,954,274 | A→C | 7.2% | E266A (GAA→GCA) ‡ | ilvD → | dihydroxy‑acid dehydratase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,049,989 | A→C | 10.8% | noncoding (91/109 nt) | spf → | small regulatory RNA Spot 42 |
| 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 | 4,296,060 | C→T | 27.7% | 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 | 4,439,845 | T→A | 8.3% | intergenic (+52/+27) | ytfK → / ← ytfL | DUF1107 domain‑containing protein YtfK/putative inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196269 | 1211448 | 15180 | 9 [8] | [7] 9 | [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 | 3621196–3622308 | 3653129–3652031 | 29724–31934 | 10 [8] | [8] 10 | [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 | = 1712803 | 25 (0.780) | 3 (0.100) | 3/246 | NT | 10.9% | coding (35/1503 nt) | dtpA | dipeptide/tripeptide:H(+) symporter DtpA |
| ? | NC_000913 | = 1712811 | 26 (0.870) | coding (43/1503 nt) | dtpA | dipeptide/tripeptide:H(+) symporter DtpA | |||||
| * | ? | NC_000913 | 4389302 = | 57 (1.770) | 3 (0.100) | 3/254 | NT | 5.8% | coding (69/3324 nt) | mscM | miniconductance mechanosensitive channel MscM |
| ? | NC_000913 | 4389328 = | 43 (1.390) | coding (43/3324 nt) | mscM | miniconductance mechanosensitive channel MscM | |||||