mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 114,992 | G→A | 13.8% | Q245* (CAG→TAG) | hofC ← | assembly protein in type IV pilin biogenesis, transmembrane protein |
| RA | 219,501 | C→T | 8.7% | A32T (GCC→ACC) | tsaA ← | tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 339,958 | G→A | 7.3% | intergenic (+215/‑207) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 417,391 | G→C | 100% | A84P (GCC→CCC) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 418,428 | Δ1 bp | 50.0% | coding (540/1296 nt) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| RA | 701,398 | T→A | 14.5% | D66V (GAT→GTT) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 702,066 | G→C | 54.8% | P229R (CCT→CGT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 906,659 | C→T | 9.0% | R32H (CGC→CAC) | ybjS ← | putative NAD(P)H‑dependent oxidoreductase |
| RA | 1,158,384 | G→A | 100% | W172* (TGG→TGA) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,196,220 | C→T | 51.4% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,232 | C→T | 51.6% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,245 | T→C | 54.6% | L375L (TTA→CTA) ‡ | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,247 | A→G | 58.1% | L375L (TTA→TTG) ‡ | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,277 | C→T | 45.8% | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,280 | G→C | 45.9% | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,283 | A→G | 47.8% | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,292 | C→T | 45.5% | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,304 | G→A | 46.2% | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,316 | T→A | 42.2% | D398E (GAT→GAA) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,325 | A→G | 42.1% | K401K (AAA→AAG) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,352 | C→A | 36.4% | D410E (GAC→GAA) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,269,766 | C→T | 8.2% | A15A (GCG→GCA) | ldrB ← | toxic polypeptide, small |
| RA | 1,269,785 | G→A | 8.3% | T9I (ACT→ATT) | ldrB ← | toxic polypeptide, small |
| 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 | 1,726,507 | Δ1 bp | 100% | coding (485/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,779,348 | Δ1 bp | 14.8% | intergenic (‑47/‑269) | ydiP ← / → ydiQ | putative DNA‑binding transcriptional regulator/putative electron transfer flavoprotein subunit |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,509,475 | A→C | 18.2% | intergenic (‑51/‑153) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,693,131 | G→A | 7.7% | A804V (GCA→GTA) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,977,594:1 | +C | 100% | coding (998/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,088,261:1 | (A)6→7 | 100% | intergenic (+403/‑21) | metK → / → galP | S‑adenosylmethionine synthetase/D‑galactose transporter |
| RA | 3,635,800 | Δ1 bp | 8.7% | coding (961/1053 nt) | yhiM → | acid resistance protein, inner membrane |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,171,647 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,451,083 | Δ1 bp | 10.8% | coding (25/1503 nt) | ytfR → | putative sugar ABC transporter ATPase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 720883 | 721170 | 288 | 8 [5] | [6] 9 | [kdpE] | [kdpE] |
| * | * | ÷ | NC_000913 | 1207806 | 1208145 | 340 | 13 [1] | [6] 8 | [stfP]–[tfaP] | [stfP], [tfaP] |
| * | * | ÷ | NC_000913 | 3423932–3424374 | 3424374 | 1–443 | 8 [6] | [6] 9 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4110725 | 4111501 | 777 | 8 [6] | [5] 7 | [tpiA] | [tpiA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 42989 = | 38 (1.120) | 3 (0.090) | 3/478 | NT | 6.9% | coding (587/771 nt) | fixA | anaerobic carnitine reduction putative electron transfer flavoprotein subunit |
| ? | NC_000913 | 43085 = | 44 (1.350) | coding (683/771 nt) | fixA | anaerobic carnitine reduction putative electron transfer flavoprotein subunit | |||||
| * | ? | NC_000913 | 95824 = | 30 (0.880) | 3 (0.090) | 3/478 | NT | 7.9% | coding (1175/1359 nt) | murF | UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase |
| ? | NC_000913 | 96344 = | 41 (1.260) | coding (343/1083 nt) | mraY | phospho‑N‑acetylmuramoyl‑pentapeptide transferase | |||||
| * | ? | NC_000913 | 153986 = | 0 (0.000) | 31 (0.910) | 27/498 | NT | 100% | coding (1441/2598 nt) | htrE | putative outer membrane usher protein |
| ? | NC_000913 | = 275149 | NA (NA) | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter | |||||
| * | ? | NC_000913 | = 153989 | 0 (0.000) | 43 (1.270) | 29/498 | NT | 100% | coding (1438/2598 nt) | htrE | putative outer membrane usher protein |
| ? | NC_000913 | 273955 = | NA (NA) | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 29 (0.860) | 24/498 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 4 (0.120) | 4/498 | NT | 10.8% | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator |
| ? | NC_000913 | 419059 = | 33 (0.970) | coding (1171/1296 nt) | phoR | sensory histidine kinase in two‑component regulatory system with PhoB | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 4 (0.120) | 4/472 | NT | NA | coding (111/300 nt) | insE1 | IS3 transposase A |
| ? | NC_000913 | 315627 = | NA (NA) | coding (41/867 nt) | insF1 | IS3 transposase B | |||||
| * | ? | NC_000913 | = 606366 | 35 (1.030) | 4 (0.120) | 3/484 | NT | 10.1% | coding (1018/1119 nt) | ybdK | weak gamma‑glutamyl:cysteine ligase |
| ? | NC_000913 | = 606463 | 37 (1.120) | coding (921/1119 nt) | ybdK | weak gamma‑glutamyl:cysteine ligase | |||||
| * | ? | NC_000913 | 759115 = | 59 (1.740) | 4 (0.120) | 4/480 | NT | 7.2% | coding (410/2802 nt) | sucA | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| ? | NC_000913 | 759344 = | 46 (1.410) | coding (639/2802 nt) | sucA | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding | |||||
| * | ? | NC_000913 | = 823202 | 34 (1.000) | 4 (0.120) | 4/486 | NT | 10.4% | coding (538/1242 nt) | clsB | cardiolipin synthase 2 |
| ? | NC_000913 | = 824344 | 36 (1.090) | coding (154/762 nt) | ybhP | endo/exonuclease/phosphatase family protein | |||||
| * | ? | NC_000913 | = 1144833 | 35 (1.030) | 4 (0.120) | 4/486 | NT | 9.5% | intergenic (+11/‑107) | yceQ/rluC | uncharacterized protein/23S rRNA pseudouridine(955,2504,2580) synthase |
| ? | NC_000913 | = 1145097 | 42 (1.270) | coding (158/960 nt) | rluC | 23S rRNA pseudouridine(955,2504,2580) synthase | |||||
| * | ? | NC_000913 | = 1207805 | 1 (0.030) | 8 (0.250) | 7/466 | NT | 89.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 1 (0.030) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.060) | 24 (0.710) | 19/498 | NT | 92.3% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 22 (0.650) | 18/498 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 25 (0.740) | 23/498 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 2016631 | 35 (1.030) | 4 (0.120) | 3/486 | NT | 13.5% | coding (78/1374 nt) | fliI | flagellum‑specific ATP synthase |
| ? | NC_000913 | = 2017005 | 17 (0.510) | coding (452/1374 nt) | fliI | flagellum‑specific ATP synthase | |||||
| * | ? | NC_000913 | = 2230412 | 40 (1.180) | 3 (0.090) | 3/482 | NT | 7.1% | intergenic (‑29/‑210) | dusC/yohJ | tRNA‑dihydrouridine synthase C/UPF0299 family inner membrane protein |
| ? | NC_000913 | = 2230415 | 40 (1.220) | intergenic (‑32/‑207) | dusC/yohJ | tRNA‑dihydrouridine synthase C/UPF0299 family inner membrane protein | |||||
| * | ? | NC_000913 | 2375822 = | 7 (0.210) | 38 (1.140) | 30/490 | NT | 84.7% | coding (139/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | = 2515611 | NA (NA) | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
| * | ? | NC_000913 | = 2375833 | 6 (0.180) | 4 (0.120) | 4/490 | NT | 40.4% | coding (128/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | 2514275 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
| * | ? | NC_000913 | 2464883 = | 19 (0.560) | 4 (0.120) | 3/488 | NT | 10.3% | coding (123/756 nt) | mlaA | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| ? | NC_000913 | 2465308 = | 51 (1.540) | coding (10/933 nt) | yfdC | putative inner membrane protein | |||||
| * | ? | NC_000913 | 2629604 = | 16 (0.470) | 3 (0.090) | 3/478 | NT | 8.4% | intergenic (+125/‑186) | yfgG/yfgH | uncharacterized protein/outer membrane integrity lipoprotein |
| ? | NC_000913 | 2630583 = | 50 (1.540) | coding (260/540 nt) | yfgI | nalidixic acid resistance protein, putative periplasmic protein | |||||
| * | ? | NC_000913 | 2791443 = | 41 (1.210) | 4 (0.120) | 4/480 | NT | 10.6% | coding (173/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| ? | NC_000913 | 2791918 = | 28 (0.860) | coding (648/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent | |||||
| * | ? | NC_000913 | = 3150653 | 23 (0.680) | 3 (0.090) | 3/478 | NT | 12.0% | noncoding (102/255 nt) | RIP222 (repetitive extragenic palindromic) element, contains 5 REP sequences and 2 IHF sites | RIP222 (repetitive extragenic palindromic) element, contains 5 REP sequences and 2 IHF sites |
| ? | NC_000913 | = 3150756 | NA (NA) | noncoding (205/255 nt) | RIP222 (repetitive extragenic palindromic) element, contains 5 REP sequences and 2 IHF sites | RIP222 (repetitive extragenic palindromic) element, contains 5 REP sequences and 2 IHF sites | |||||
| * | ? | NC_000913 | = 4327974 | 28 (0.830) | 4 (0.120) | 3/482 | NT | 11.9% | coding (839/2229 nt) | crfC | clamp‑binding sister replication fork colocalization protein, dynamin‑related |
| ? | NC_000913 | = 4328276 | 32 (0.980) | coding (1141/2229 nt) | crfC | clamp‑binding sister replication fork colocalization protein, dynamin‑related | |||||
| * | ? | NC_000913 | = 4553754 | 21 (0.620) | 3 (0.090) | 3/468 | NT | 8.5% | coding (853/1461 nt) | uxuB | D‑mannonate oxidoreductase, NAD‑dependent |
| ? | NC_000913 | = 4554836 | 45 (1.410) | coding (260/774 nt) | uxuR | fructuronate‑inducible hexuronate regulon transcriptional repressor, autorepressor | |||||
| * | ? | NC_000913 | 4558976 = | 45 (1.330) | 3 (0.090) | 3/480 | NT | 6.6% | coding (552/1173 nt) | iadA | isoaspartyl dipeptidase |
| ? | NC_000913 | 4559022 = | 41 (1.260) | coding (506/1173 nt) | iadA | isoaspartyl dipeptidase | |||||
| * | ? | NC_000913 | 4602976 = | 26 (0.770) | 4 (0.120) | 4/484 | NT | 14.5% | intergenic (‑117/‑502) | yjjP/yjjQ | DUF1212 family inner membrane protein/putative transcriptional regulator |
| ? | NC_000913 | 4603101 = | 22 (0.670) | intergenic (‑242/‑377) | yjjP/yjjQ | DUF1212 family inner membrane protein/putative transcriptional regulator | |||||