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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| 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 | |
| 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 | 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 |
| RA | 3,815,810 | Δ1 bp | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 4,233,772 | G→T | intergenic (‑539/‑2135) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,408 | Δ1 bp | intergenic (‑2175/‑499) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_bme_pgi | 607411 | 607446 | 36 | 2 [0] | [1] 3 | ybdK/sokE | weak gamma‑glutamyl:cysteine ligase/sRNA at remnant mokE/hokE locus |
| * | * | ÷ | NC_000913_3_bme_pgi | 653463 | 653497 | 35 | 2 [1] | [1] 2 | citA | sensory histidine kinase in two‑component regulatory system with CitB |
| * | * | ÷ | NC_000913_3_bme_pgi | 889666 | 889712 | 47 | 2 [1] | [1] 2 | ybjL | putative transporter |
| * | * | ÷ | NC_000913_3_bme_pgi | 1092202 | 1092213 | 12 | 2 [0] | [0] 2 | pgaA | biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein |
| * | * | ÷ | NC_000913_3_bme_pgi | 1155437 | 1155473 | 37 | 2 [0] | [1] 2 | tmk | thymidylate kinase |
| * | * | ÷ | NC_000913_3_bme_pgi | 1209603 | 1209618 | 16 | 8 [0] | [0] 18 | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| * | * | ÷ | NC_000913_3_bme_pgi | 1285203 | 1285219 | 17 | 4 [0] | [1] 3 | narJ | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 |
| * | * | ÷ | NC_000913_3_bme_pgi | 1528461–1529167 | 1529206 | 40–746 | 2 [1] | [1] 3 | rhsE | pseudogene, Rhs family |
| * | * | ÷ | NC_000913_3_bme_pgi | 2382702 | 2382725 | 24 | 3 [1] | [0] 2 | [elaD] | [elaD] |
| * | * | ÷ | NC_000913_3_bme_pgi | 3299633 | 3299644 | 12 | 3 [0] | [1] 2 | yhbP | UPF0306 family protein |
| * | * | ÷ | NC_000913_3_bme_pgi | 3423789–3424234 | 3424558–3424240 | 7–770 | 2 [1] | [1] 3 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913_3_bme_pgi | 3681458 | 3681515 | 58 | 2 [1] | [1] 3 | yhjJ | putative periplasmic M16 family chaperone |
| * | * | ÷ | NC_000913_3_bme_pgi | 3778448 | 3778467 | 20 | 2 [0] | [1] 3 | lldP | L‑lactate permease |
| * | * | ÷ | NC_000913_3_bme_pgi | 3914110 | 3914194 | 85 | 2 [1] | [1] 2 | glmU | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase |
| * | * | ÷ | NC_000913_3_bme_pgi | 4391919 | 4391950 | 32 | 2 [1] | [0] 2 | orn | oligoribonuclease |
| * | * | ÷ | NC_000913_3_bme_pgi | 4496720 | 4496752 | 33 | 3 [1] | [1] 3 | intB | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_bme_pgi | 1207790 = | 2 (0.140) | 16 (1.270) | 15/228 | 0.1 | 94.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | 1209619 = | 0 (0.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1207805 | 2 (0.140) | 8 (0.630) | 8/228 | 0.6 | 90.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | = 1209602 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1357753 | NA (NA) | 4 (0.300) | 4/242 | 1.3 | NA | intergenic (‑85/+49) | ymjA/puuP | DUF2543 family protein/putrescine importer |
| ? | NC_000913_3_bme_pgi | = 1357792 | NA (NA) | noncoding (23/30 nt) | REP111 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP111 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | = 1529619 | 15 (1.040) | 4 (0.290) | 4/250 | 1.4 | 21.4% | pseudogene (1718/2037 nt) | rhsE | pseudogene, Rhs family |
| ? | NC_000913_3_bme_pgi | = 1529633 | 15 (1.080) | pseudogene (1732/2037 nt) | rhsE | pseudogene, Rhs family | |||||
| * | ? | NC_000913_3_bme_pgi | = 3319994 | 15 (1.040) | 4 (0.290) | 4/250 | 1.4 | 22.6% | coding (1620/1626 nt) | yhbX | putative EptAB family phosphoethanolamine transferase, inner membrane protein |
| ? | NC_000913_3_bme_pgi | = 3320009 | 13 (0.940) | coding (1605/1626 nt) | yhbX | putative EptAB family phosphoethanolamine transferase, inner membrane protein | |||||
| * | ? | NC_000913_3_bme_pgi | 3566202 = | 14 (0.970) | 4 (0.300) | 3/244 | 1.6 | 24.1% | coding (380/2448 nt) | glgP | glycogen phosphorylase |
| ? | NC_000913_3_bme_pgi | 3566229 = | 12 (0.890) | coding (353/2448 nt) | glgP | glycogen phosphorylase | |||||
| * | ? | NC_000913_3_bme_pgi | 3652037 = | NA (NA) | 11 (0.770) | 10/258 | 0.5 | 100% | intergenic (+6/+145) | yhiS/insH1 | pseudogene/IS5 transposase and trans‑activator |
| ? | NC_000913_3_bme_pgi | = 3992709 | 0 (0.000) | coding (1557/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913_3_bme_pgi | = 3653229 | NA (NA) | 12 (0.840) | 12/258 | 0.3 | 100% | intergenic (‑31/‑2) | insH1/yhiS | IS5 transposase and trans‑activator/pseudogene |
| ? | NC_000913_3_bme_pgi | 3992704 = | 0 (0.000) | coding (1552/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913_3_bme_pgi | 4239741 = | 14 (0.970) | 3 (0.230) | 3/238 | 1.6 | 20.8% | intergenic (+10/+37) | yjbH/yjbT | DUF940 family extracellular polysaccharide protein/putative periplasmic protein |
| ? | NC_000913_3_bme_pgi | 4239773 = | 10 (0.760) | intergenic (+42/+5) | yjbH/yjbT | DUF940 family extracellular polysaccharide protein/putative periplasmic protein | |||||
| * | ? | NC_000913_3_bme_pgi | 4542683 = | 13 (0.900) | 8 (0.600) | 8/242 | 0.6 | 40.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_bme_pgi | 4542997 = | 11 (0.820) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||