mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 278,652 | G→T | 6.7% | L51M (CTG→ATG) | afuC ← | CP4‑6 prophage; putative ferric transporter subunit |
| RA | 320,423 | T→G | 12.9% | V66G (GTG→GGG) | rclR → | reactive chlorine species (RCS)‑specific activator of the rcl genes |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 100% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 525,571 | T→G | 14.9% | W771G (TGG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 540,546 | C→T | 12.5% | intergenic (+38/‑19) | allB → / → ybbY | allantoinase/putative uracil/xanthine transporter |
| RA | 1,061,965 | A→G | 35.1% | E56G (GAG→GGG) | torD → | TorA‑maturation chaperone |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | 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 | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,445,981 | T→G | 31.7% | G34G (GGT→GGG) | ydbL → | DUF1318 family protein |
| JC | 1,707,847 | Δ10 bp | 19.1% | coding (929‑938/2223 nt) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,709,179:1 | +C | 14.3% | coding (38/1059 nt) | rsxD → | SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex |
| RA | 1,878,707 | A→C | 10.9% | T331T (ACA→ACC) | yeaP → | diguanylate cyclase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,104,337 | T→C | 7.7% | E58G (GAG→GGG) | wbbK ← | lipopolysaccharide biosynthesis protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,283,059 | C→A | 13.6% | D297Y (GAT→TAT) | yejK ← | spermidine nucleoid‑associated protein |
| JC | 2,391,259 | +CAA | 12.1% | coding (247/1458 nt) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 3,277,448 | G→A | 17.2% | E38K (GAA→AAA) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,289,078 | C→A | 21.9% | Q89K (CAG→AAG) | yraJ → | putative outer membrane protein |
| RA | 3,327,171 | A→C | 15.1% | V165G (GTG→GGG) | rlmE ← | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,335,254 | T→C | 12.7% | E414G (GAG→GGG) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| JC | 3,399,171 | Δ3 bp | 7.1% | coding (806‑808/1104 nt) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
| RA | 3,507,168 | T→C | 15.7% | S57G (AGC→GGC) | yhfT ← | inner membrane protein |
| JC JC | 3,560,227 | IS5 (–) +4 bp | 8.9% | pseudogene (224‑227/606 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,638,228 | A→G | 23.5% | E196G (GAG→GGG) | pitA → | phosphate transporter, low‑affinity; tellurite importer |
| RA | 3,697,740 | T→G | 15.7% | V428G (GTG→GGG) | bcsE → | cellulose production protein |
| RA | 3,699,266 | T→A | 7.1% | N351K (AAT→AAA) | bcsG → | DUF3260 family cellulose production inner membrane protein |
| RA | 3,791,999 | A→G | 7.2% | S185P (TCA→CCA) | kbl ← | glycine C‑acetyltransferase |
| RA | 3,792,340 | G→A | 10.2% | S71F (TCT→TTT) | kbl ← | glycine C‑acetyltransferase |
| RA | 3,796,793 | A→G | 13.2% | D272G (GAT→GGT) | waaC → | ADP‑heptose:LPS heptosyl transferase I |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,817,496 | T→G | 10.7% | V274G (GTG→GGG) | yicC → | UPF0701 family protein |
| RA | 3,832,077 | G→A | 5.8% | V541M (GTG→ATG) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,056,115 | A→C | 20.7% | G75G (GGT→GGG) | glnL ← | sensory histidine kinase in two‑component regulatory system with GlnG |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,242,022 | C→A | 12.2% | C78F (TGC→TTC) | xylE ← | D‑xylose transporter |
| RA | 4,268,202 | T→G | 6.5% | R363R (CGT→CGG) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,277,820 | G→T | 6.4% | G118* (GGA→TGA) | soxR → | redox‑sensitive transcriptional activator of soxS; autorepressor |
| RA | 4,296,060 | C→T | 20.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,319,404 | A→C | 22.9% | V68G (GTG→GGG) | phnJ ← | carbon‑phosphorus lyase, SAM‑dependent |
| RA | 4,368,930 | C→T | 11.5% | G89G (GGC→GGT) | fxsA → | suppressor of F exclusion of phage T7 |
| RA | 4,378,890 | C→A | 23.8% | A19S (GCT→TCT) | ampC ← | penicillin‑binding protein; beta‑lactamase, intrinsically weak |
| RA | 4,530,174 | T→A | 12.0% | I24F (ATC→TTC) | sgcC ← | putative PTS system EIIC permease component |
| RA | 4,588,079 | A→C | 20.1% | W263G (TGG→GGG) | yjiA ← | metal‑binding GTPase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 384825 | 385029 | 205 | 17 [11] | [10] 15 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1465098 | 1465315 | 218 | 14 [13] | [13] 14 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 2469267 | 2469547 | 281 | 15 [13] | [10] 14 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 3799035 | 3799352 | 318 | 17 [9] | [12] 14 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 4233776 | 4235396 | 1621 | 14 [13] | [12] 20 | pgi | glucosephosphate isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 21 (0.290) | 81 (1.210) | 58/378 | NT | 85.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.130) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 20 (0.270) | 53 (0.790) | 41/378 | NT | 79.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1710417 | 37 (0.510) | 3 (0.040) | 3/408 | NT | 7.5% | coding (214/621 nt) | rsxG | SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||