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 | 198,073 | G→A | 5.8% | R49H (CGC→CAC) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 468,263 | G→A | 7.1% | intergenic (+33/‑120) | cof → / → ybaO | thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase/putative DNA‑binding transcriptional regulator |
| RA | 526,792 | A→C | 30.2% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,796 | C→G | 33.5% | A1179G (GCG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 29.8% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 569,862 | G→A | 5.8% | V321I (GTA→ATA) | ybcK → | DLP12 prophage; putative recombinase |
| RA | 1,376,811 | C→T | 10.5% | R260C (CGT→TGT) | ycjR → | putative TIM alpha/beta barrel enzyme |
| RA | 1,715,794 | G→A | 9.5% | N32N (AAC→AAT) | pdxY ← | pyridoxamine kinase |
| RA | 1,971,929 | A→C | 8.6% | S255A (TCA→GCA) | tar ← | methyl‑accepting chemotaxis protein II |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,665,522 | A→G | 6.8% | T30A (ACC→GCC) | csiE → | stationary phase inducible protein |
| RA | 2,817,877 | C→T | 14.4% | intergenic (‑17/+182) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 3,486,574 | C→A | 100% | A152E (GCA→GAA) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| 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 |
| JC | 3,815,859 | Δ82 bp | 67.5% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,966,742 | G→T | 22.8% | R109L (CGC→CTC) | rho → | transcription termination factor |
| RA | 4,233,708 | C→T | 100% | intergenic (‑475/‑2199) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,233,793 | C→T | 9.7% | intergenic (‑560/‑2114) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,407 | Δ1 bp | 100% | intergenic (‑2174/‑500) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,296,061 | C→T | 16.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,381:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,401,467 | G→A | 9.1% | A265A (GCG→GCA) | hflX → | GTPase, stimulated by 50S subunit binding; Mn(2+) homeostasis regulator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_bme_pgi | 366200 | 366411 | 212 | 16 [14] | [14] 17 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913_3_bme_pgi | 1528411–1529178 | 1529219 | 42–809 | 16 [15] | [14] 16 | rhsE | pseudogene, Rhs family |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_bme_pgi | 224150 = | NA (NA) | 4 (0.090) | 4/266 | NT | NA | noncoding (380/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_bme_pgi | 224171 = | NA (NA) | noncoding (401/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_bme_pgi | 316042 = | NA (NA) | 3 (0.070) | 3/262 | NT | NA | coding (456/867 nt) | insF1 | IS3 transposase B |
| ? | NC_000913_3_bme_pgi | 316055 = | NA (NA) | coding (469/867 nt) | insF1 | IS3 transposase B | |||||
| * | ? | NC_000913_3_bme_pgi | 463838 = | 30 (0.640) | 3 (0.070) | 3/266 | NT | 9.3% | intergenic (+52/‑99) | ppiD/ybaV | periplasmic folding chaperone, has an inactive PPIase domain/putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein |
| ? | NC_000913_3_bme_pgi | 463848 = | 29 (0.640) | intergenic (+62/‑89) | ppiD/ybaV | periplasmic folding chaperone, has an inactive PPIase domain/putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein | |||||
| * | ? | NC_000913_3_bme_pgi | = 872429 | 46 (0.990) | 3 (0.070) | 3/262 | NT | 6.3% | coding (540/912 nt) | gsiD | glutathione ABC transporter permease |
| ? | NC_000913_3_bme_pgi | = 872441 | 45 (1.000) | coding (552/912 nt) | gsiD | glutathione ABC transporter permease | |||||
| * | ? | NC_000913_3_bme_pgi | = 1084764 | NA (NA) | 4 (0.090) | 3/264 | NT | NA | noncoding (83/86 nt) | REP95 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP95 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_bme_pgi | 3098440 = | NA (NA) | noncoding (28/121 nt) | REP217 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP217 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | 1207790 = | 7 (0.150) | 35 (0.850) | 32/240 | NT | 78.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | 1209619 = | 13 (0.320) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1207805 | 7 (0.150) | 35 (0.850) | 31/240 | NT | 78.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | = 1209602 | 13 (0.320) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1299498 | 0 (0.000) | 43 (0.950) | 38/264 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_bme_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_bme_pgi | 1333674 = | 49 (1.050) | 3 (0.070) | 3/260 | NT | 6.1% | intergenic (+29/‑181) | topA/cysB | DNA topoisomerase I, omega subunit/N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor |
| ? | NC_000913_3_bme_pgi | 1333698 = | 45 (1.010) | intergenic (+53/‑157) | topA/cysB | DNA topoisomerase I, omega subunit/N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor | |||||
| * | ? | NC_000913_3_bme_pgi | = 1343169 | 43 (0.920) | 3 (0.060) | 3/272 | NT | 6.5% | coding (160/219 nt) | osmB | osmotically and stress inducible lipoprotein |
| ? | NC_000913_3_bme_pgi | = 1343191 | 44 (0.940) | coding (138/219 nt) | osmB | osmotically and stress inducible lipoprotein | |||||
| * | ? | NC_000913_3_bme_pgi | 2095931 = | 23 (0.490) | 3 (0.070) | 3/268 | NT | 9.4% | coding (88/777 nt) | hisF | imidazole glycerol phosphate synthase, catalytic subunit with HisH |
| ? | NC_000913_3_bme_pgi | 2096003 = | 35 (0.760) | coding (160/777 nt) | hisF | imidazole glycerol phosphate synthase, catalytic subunit with HisH | |||||
| * | ? | NC_000913_3_bme_pgi | 2279413 = | 41 (0.880) | 3 (0.070) | 3/260 | NT | 7.2% | coding (348/1191 nt) | bcr | bicyclomycin/cysteine/sulfonamide efflux transporter |
| ? | NC_000913_3_bme_pgi | 2279435 = | 38 (0.850) | coding (326/1191 nt) | bcr | bicyclomycin/cysteine/sulfonamide efflux transporter | |||||
| * | ? | NC_000913_3_bme_pgi | 2304480 = | 26 (0.560) | 5 (0.110) | 5/262 | NT | 18.2% | noncoding (64/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913_3_bme_pgi | 2304946 = | 20 (0.450) | noncoding (530/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | = 2475050 | 49 (1.050) | 4 (0.090) | 4/268 | NT | 7.4% | coding (67/537 nt) | yfdR | CPS‑53 (KpLE1) prophage; conserved protein |
| ? | NC_000913_3_bme_pgi | = 2475065 | 52 (1.130) | coding (82/537 nt) | yfdR | CPS‑53 (KpLE1) prophage; conserved protein | |||||
| * | ? | NC_000913_3_bme_pgi | 2549484 = | NA (NA) | 3 (0.070) | 3/258 | NT | NA | noncoding (19/98 nt) | RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_bme_pgi | 3563589 = | NA (NA) | noncoding (8/98 nt) | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP256 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_bme_pgi | 2726200 = | NA (NA) | 3 (0.070) | 3/260 | NT | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_bme_pgi | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_bme_pgi | = 2779754 | 36 (0.770) | 3 (0.070) | 3/258 | NT | 7.9% | coding (2973/4581 nt) | ypjA | adhesin‑like autotransporter |
| ? | NC_000913_3_bme_pgi | = 2779757 | 36 (0.810) | coding (2970/4581 nt) | ypjA | adhesin‑like autotransporter | |||||
| * | ? | NC_000913_3_bme_pgi | = 3092488 | 30 (0.640) | 4 (0.090) | 4/262 | NT | 11.6% | coding (611/951 nt) | gshB | glutathione synthetase |
| ? | NC_000913_3_bme_pgi | = 3092493 | 32 (0.710) | coding (616/951 nt) | gshB | glutathione synthetase | |||||
| * | ? | NC_000913_3_bme_pgi | = 3402416 | 54 (1.160) | 3 (0.070) | 3/260 | NT | 5.4% | coding (917/1941 nt) | csrD | targeting factor for csrBC sRNA degradation |
| ? | NC_000913_3_bme_pgi | = 3402431 | 54 (1.210) | coding (902/1941 nt) | csrD | targeting factor for csrBC sRNA degradation | |||||
| * | ? | NC_000913_3_bme_pgi | = 3828619 | 29 (0.620) | 3 (0.070) | 3/260 | NT | 9.6% | coding (47/1206 nt) | gltS | glutamate transporter |
| ? | NC_000913_3_bme_pgi | = 3828623 | 29 (0.650) | coding (43/1206 nt) | gltS | glutamate transporter | |||||
| * | ? | NC_000913_3_bme_pgi | 4150468 = | 58 (1.240) | 3 (0.070) | 3/262 | NT | 5.3% | coding (2631/2652 nt) | ppc | phosphoenolpyruvate carboxylase |
| ? | NC_000913_3_bme_pgi | 4150484 = | 52 (1.160) | coding (2615/2652 nt) | ppc | phosphoenolpyruvate carboxylase | |||||
| * | ? | NC_000913_3_bme_pgi | 4315761 = | 58 (1.240) | 3 (0.070) | 3/258 | NT | 5.3% | coding (323/558 nt) | phnN | ribose 1,5‑bisphosphokinase |
| ? | NC_000913_3_bme_pgi | 4315790 = | 53 (1.200) | coding (294/558 nt) | phnN | ribose 1,5‑bisphosphokinase | |||||