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 | 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 | 756,792 | G→T | 68.6% | 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 | |
| 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 | 59.7% | S6N (AGC→AAC) | yfdE ← | acetyl‑CoA:oxalate CoA‑transferase |
| RA | 2,775,085 | T→C | 10.4% | intergenic (+64/‑460) | yfjW → / → ypjI | CP4‑57 prophage; uncharacterized protein YfjW/putative UPF0401 protein YpjI |
| RA | 2,775,089 | T→A | 10.3% | intergenic (+68/‑456) | yfjW → / → ypjI | CP4‑57 prophage; uncharacterized protein YfjW/putative UPF0401 protein YpjI |
| RA | 2,775,093 | G→A | 10.6% | intergenic (+72/‑452) | yfjW → / → ypjI | CP4‑57 prophage; uncharacterized protein YfjW/putative UPF0401 protein YpjI |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,156,590 | C→A | 22.9% | intergenic (+72/‑33) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,156,591 | T→G | 23.4% | intergenic (+73/‑32) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,389,186 | T→C | 64.9% | 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] | |
| JC | 3,992,517 | Δ5 bp | 11.9% | coding (1365‑1369/2547 nt) | cyaA → | adenylate cyclase |
| JC | 4,001,645 | Δ5 bp | 90.0% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,270,146 | T→C | 6.1% | intergenic (+19/‑92) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/UPF0047 protein YjbQ |
| RA | 4,287,423:1 | +T | 76.9% | intergenic (‑52/‑341) | acs ← / → nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| RA | 4,296,060 | C→T | 21.3% | 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 | 4,314,233 | A→T | 8.4% | intergenic (+36/+111) | yjdP → / ← phnP | protein YjdP/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| RA | 4,409,407 | T→A | 7.2% | S45T (TCT→ACT) | rlmB → | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196277 | 1211437 | 15161 | 7 [6] | [6] 7 | [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 | 3621180–3622297 | 3653115–3652030 | 29734–31936 | 7 [6] | [6] 7 | [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 | = 732302 | 19 (0.680) | 3 (0.110) | 3/252 | NT | 14.6% | coding (2720/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | = 732308 | 17 (0.630) | coding (2726/4194 nt) | rhsC | rhs element protein RhsC | |||||
| * | ? | NC_000913 | = 1437207 | 38 (1.350) | 3 (0.110) | 3/250 | NT | 7.9% | noncoding (87/109 nt) | micC | small regulatory RNA MicC |
| ? | NC_000913 | = 1437217 | 34 (1.280) | noncoding (97/109 nt) | micC | small regulatory RNA MicC | |||||
| * | ? | NC_000913 | = 1899959 | 26 (0.930) | 3 (0.110) | 3/252 | NT | 10.8% | coding (1533/1599 nt) | pdeD | putative c‑di‑GMP phosphodiesterase PdeD |
| ? | NC_000913 | = 1899964 | 25 (0.930) | coding (1538/1599 nt) | pdeD | putative c‑di‑GMP phosphodiesterase PdeD | |||||
| * | ? | NC_000913 | = 2306358 | 21 (0.750) | 3 (0.110) | 3/258 | NT | 13.8% | coding (397/1647 nt) | mqo | malate:quinone oxidoreductase |
| ? | NC_000913 | = 2306383 | 17 (0.620) | coding (372/1647 nt) | mqo | malate:quinone oxidoreductase | |||||
| * | ? | NC_000913 | 4542682 = | 23 (0.820) | 7 (0.270) | 7/246 | NT | 26.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 18 (0.690) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 23 (0.820) | 12 (0.460) | 12/246 | NT | 37.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 18 (0.690) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||