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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| JC JC | 1,293,032 | IS1 (–) +8 bp | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,862,760 | C→T | R142R (CGC→CGT) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 3,560,455 | +G | 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 |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | 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 | 761494 | 762730 | 1237 | 6 [4] | [5] 6 | [sucA]–[sucB] | [sucA],[sucB] |
| * | * | ÷ | NC_000913 | 1882527 | 1882600 | 74 | 8 [4] | [5] 6 | dmlA | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
| * | * | ÷ | NC_000913 | 3423762–3424234 | 3424529–3424239 | 6–768 | 7 [4] | [4] 6 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 225281 | NA (NA) | 9 (0.260) | 9/238 | 2.1 | NA | noncoding (1511/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 225293 | NA (NA) | noncoding (1523/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 6 (0.180) | 6/230 | 2.7 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 315563 = | NA (NA) | 5 (0.150) | 5/228 | 2.9 | NA | noncoding (335/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315599 = | NA (NA) | noncoding (371/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 756106 = | 9 (0.250) | 25 (0.720) | 21/240 | 0.7 | 82.4% | coding (200/1767 nt) | sdhA | succinate dehydrogenase, flavoprotein subunit |
| ? | NC_000913 | 756221 = | 2 (0.060) | coding (315/1767 nt) | sdhA | succinate dehydrogenase, flavoprotein subunit | |||||
| * | ? | NC_000913 | = 756109 | 9 (0.250) | 15 (0.430) | 14/240 | 1.3 | 73.7% | coding (203/1767 nt) | sdhA | succinate dehydrogenase, flavoprotein subunit |
| ? | NC_000913 | = 756216 | 2 (0.060) | coding (310/1767 nt) | sdhA | succinate dehydrogenase, flavoprotein subunit | |||||
| * | ? | NC_000913 | 856550 = | 25 (0.700) | 8 (0.240) | 8/234 | 2.2 | 26.0% | coding (588/1593 nt) | ybiT | ABC‑F family putative regulatory ATPase |
| ? | NC_000913 | 856575 = | 22 (0.650) | coding (613/1593 nt) | ybiT | ABC‑F family putative regulatory ATPase | |||||
| * | ? | NC_000913 | 1207790 = | 0 (0.000) | 28 (0.900) | 26/216 | 0.3 | 91.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 5 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 0 (0.000) | 26 (0.840) | 25/216 | 0.3 | 91.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 5 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2805380 | 20 (0.560) | 6 (0.180) | 5/230 | 3.0 | 22.4% | coding (566/1203 nt) | proV | glycine betaine/proline ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 2805401 | 23 (0.700) | coding (587/1203 nt) | proV | glycine betaine/proline ABC transporter periplasmic binding protein | |||||