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 | seq id | position | mutation | annotation | gene | description |
| RA | BN000925 | 9,791 | A→G | D797G (GAC→GGC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 9,802 | G→A | D801N (GAC→AAC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,089 | A→C | A896A (GCA→GCC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,359 | T→A | G986G (GGT→GGA) | tnpA → | Tn1 transposase |
| RA | BN000925 | 12,239 | +A | intergenic (‑601/+1055) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,406 | T→G | intergenic (‑768/+888) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,688 | T→A | intergenic (‑1050/+606) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 13,638 | T→C | T103A (ACG→GCG) | tetR ← | tetracycline resistance repressor protein |
| RA | BN000925 | 15,561 | Δ1 bp | intergenic (+312/+320) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,639 | C→G | intergenic (+390/+242) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,898 | +C | coding (649/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 16,410 | +T | coding (137/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 17,615 | A→C | F19V (TTT→GTT) | trfA ← | TrfA replication protein |
| RA | BN000925 | 25,464 | T→C | F71L (TTT→CTT) | trbI → | TrbI protein |
| RA | BN000925 | 31,028 | C→G | P35A (CCC→GCC) | trbP → | TrbP protein |
| RA | BN000925 | 36,655 | A→G | R116G (AGA→GGA) R108G (AGA→GGA) |
istA → istA → |
IS21 transposase IS21 transposase |
| RA | BN000925 | 38,388 | A→C | pseudogene (45/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,390 | 1 bp→AG | pseudogene (47/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,393 | C→T | pseudogene (50/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,421 | Δ1 bp | pseudogene (78/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,510 | Δ1 bp | pseudogene (167/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,526 | Δ1 bp | intergenic (+12/‑232) | upf35.8 → / → aphA | probable truncation of theoretical product due to sequence errors/aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,136 | Δ1 bp | coding (379/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,147 | Δ1 bp | coding (390/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,179 | +CG | coding (422/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 53,069 | +T | intergenic (+42/+10) | traM → / ← kfrC | TraM protein/KfrC protein |
| RA | BN000925 | 54,833 | Δ1 bp | intergenic (‑32/+127) | kfrB ← / ← kfrA | KfrB protein/KfrA coiled‑coil protein |
| RA | BN000925 | 56,817 | Δ1 bp | coding (297/522 nt) | korF ← | KorF repressor protein |
| RA | NC_000913 | 31,826 | A→G | N337S (AAC→AGC) | carB → | carbamoyl phosphate synthetase subunit beta |
| RA | NC_000913 | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl phosphate synthetase subunit beta/DNA‑binding transcriptional activator CaiF |
| RA | NC_000913 | 43,799 | T→C | G204G (GGT→GGC) | fixB → | putative electron transfer flavoprotein FixB |
| RA | NC_000913 | 72,499 | A→G | C143C (TGT→TGC) | thiQ ← | thiamine ABC transporter ATP binding subunit |
| RA | NC_000913 | 82,095 | Δ1 bp | coding (1435/1572 nt) | leuA ← | 2‑isopropylmalate synthase |
| RA | NC_000913 | 117,029 | A→G | V24A (GTG→GCG) | hofB ← | T2SSE family protein |
| RA | NC_000913 | 212,579 | G→A | A83A (GCG→GCA) | tilS → | tRNA(Ile)‑lysidine synthetase |
| MC JC | NC_000913 | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | NC_000913 | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | NC_000913 | 309,293 | A→G | F14L (TTT→CTT) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | NC_000913 | 368,328 | A→G | G31G (GGT→GGC) | mhpR ← | DNA‑binding transcriptional activator MhpR |
| RA | NC_000913 | 486,305 | Δ1 bp | coding (545/648 nt) | acrR → | DNA‑binding transcriptional repressor AcrR |
| RA | NC_000913 | 515,440 | T→G | T112P (ACC→CCC) | qmcA ← | PHB domain‑containing protein |
| RA | NC_000913 | 534,074 | T→C | G53G (GGT→GGC) | gcl → | glyoxylate carboligase |
| RA | NC_000913 | 559,919 | A→G | N75D (AAT→GAT) | sfmD → | putative fimbrial usher protein SfmD |
| RA | NC_000913 | 603,413 | (T)7→8 | intergenic (+78/+3) | pheP → / ← ybdG | phenylalanine:H(+) symporter PheP/miniconductance mechanosensitive channel YbdG |
| RA | NC_000913 | 609,147 | (C)7→8 | coding (1083/1113 nt) | insL‑2 → | IS186/IS421 transposase |
| RA | NC_000913 | 693,260 | A→G | I40T (ATC→ACC) | ybeZ ← | PhoH‑like protein |
| RA | NC_000913 | 798,716 | G→A | S44N (AGC→AAC) | pgl → | 6‑phosphogluconolactonase |
| RA | NC_000913 | 810,751 | A→G | D124G (GAC→GGC) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | NC_000913 | 813,776 | A→G | N84S (AAC→AGC) | uvrB → | excision nuclease subunit B |
| RA | NC_000913 | 994,045 | A→G | V263A (GTA→GCA) | ssuC ← | aliphatic sulfonate ABC transporter membrane subunit |
| RA | NC_000913 | 1,146,978 | A→G | N62S (AAC→AGC) | yceD → | DUF177 domain‑containing protein YceD |
| RA | NC_000913 | 1,152,970 | T→C | G344G (GGT→GGC) | fabF → | beta‑ketoacyl‑[acyl carrier protein] synthase II |
| RA | NC_000913 | 1,176,925 | A→G | T103A (ACC→GCC) | lolD → | lipoprotein release complex ‑ ATP binding subunit |
| RA | NC_000913 | 1,212,088 | (C)8→7 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | NC_000913 | 1,223,984 | (A)7→6 | intergenic (+77/+295) | ycgI → / ← minE | protein YcgI/Z‑ring positioning protein MinE |
| RA | NC_000913 | 1,245,040 | T→C | intergenic (+58/‑120) | ymgE → / → ycgY | PF04226 family protein YmgE/uncharacterized protein YcgY |
| RA | NC_000913 | 1,248,336 | G→A | A260V (GCC→GTC) | dhaM ← | dihydroxyacetone kinase subunit M |
| RA | NC_000913 | 1,259,002 | A→G | D71G (GAC→GGC) | ychH → | stress‑induced protein |
| RA | NC_000913 | 1,296,375 | A→G | F583L (TTC→CTC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | NC_000913 | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | NC_000913 | 1,440,164 | T→C | E207E (GAA→GAG) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | NC_000913 | 1,444,766 | T→C | P572P (CCT→CCC) | ydbH → | PF11739 family protein YdbH |
| RA | NC_000913 | 1,522,923 | C→T | S48N (AGC→AAC) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | NC_000913 | 1,684,830 | A→G | E191G (GAA→GGA) | tus → | DNA replication terminus site‑binding protein |
| RA | NC_000913 | 2,028,371 | A→G | intergenic (‑1/+78) | yodC ← / ← yedI | protein YodC/conserved inner membrane protein YedI |
| RA | NC_000913 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | NC_000913 | 2,185,875 | (G)7→8 | intergenic (‑79/‑42) | rcnR ← / → rcnA | DNA‑binding transcriptional repressor RcnR/Ni(2(+))/Co(2(+)) exporter |
| RA | NC_000913 | 2,249,587 | A→T | F11Y (TTT→TAT) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | NC_000913 | 2,263,380 | T→C | Y39C (TAC→TGC) | fruB ← | fructose‑specific PTS multiphosphoryl transfer protein FruB |
| RA | NC_000913 | 2,291,845 | T→C | D189G (GAC→GGC) | ccmH ← | holocytochrome c synthetase ‑ thiol:disulfide oxidoreductase CcmH |
| RA | NC_000913 | 2,297,114 | (C)7→8 | coding (531/624 nt) | ccmA ← | heme trafficking system ATP‑binding protein |
| RA | NC_000913 | 2,448,637 | A→G | D11G (GAC→GGC) | smrB → | putative endonuclease SmrB |
| RA | NC_000913 | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | NC_000913 | 2,653,536 | G→A | intergenic (+197/‑319) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/small regulatory RNA RyfA |
| RA | NC_000913 | 2,667,580 | (C)5→4 | coding (267/1140 nt) | hcaT ← | putative 3‑phenylpropionate transporter |
| RA | NC_000913 | 2,741,620 | T→C | G87G (GGT→GGC) | yfiL → | DUF2799 domain‑containing lipoprotein YfiL |
| RA | NC_000913 | 2,763,916 | C→T | R413Q (CGG→CAG) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | NC_000913 | 2,769,121 | (G)5→6 | coding (457/822 nt) | yfjQ → | CP4‑57 prophage; protein YfjQ |
| RA | NC_000913 | 2,854,667 | A→G | A110A (GCA→GCG) | fhlA → | DNA‑binding transcriptional activator FhlA |
| RA | NC_000913 | 2,905,219 | (C)6→7 | coding (200/672 nt) | queE ← | putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | NC_000913 | 2,972,909 | (C)6→7 | coding (954/1194 nt) | lplT ← | lysophospholipid transporter |
| RA | NC_000913 | 3,192,161 | T→C | intergenic (‑222/‑47) | glgS ← / → yqiJ | surface composition regulator/putative inner membrane protein |
| RA | NC_000913 | 3,211,010 | T→C | intergenic (+14/‑97) | rpsU → / → dnaG | 30S ribosomal subunit protein S21/DNA primase |
| RA | NC_000913 | 3,307,424 | T→C | D146G (GAC→GGC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| MC JC | NC_000913 | 3,366,751 | Δ295 bp | IS5‑mediated | yhcE–[yhcF] | yhcE, [yhcF] |
| RA | NC_000913 | 3,530,108 | A→G | Y112C (TAC→TGC) | hslO → | molecular chaperone Hsp33 |
| RA | NC_000913 | 3,535,723 | A→G | V49A (GTC→GCC) | envZ ← | sensory histidine kinase EnvZ |
| RA | NC_000913 | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | NC_000913 | 3,686,880 | T→C | D765G (GAC→GGC) | bcsC ← | cellulose biosynthesis protein BcsC |
| RA | NC_000913 | 3,705,229 | C→T | D188N (GAC→AAC) | dppB ← | dipeptide ABC transporter membrane subunit DppB |
| RA | NC_000913 | 3,717,751 | C→T | L148L (CTG→TTG) | ghrB → | glyoxylate reductase |
| RA | NC_000913 | 3,760,132 | (G)6→8 | coding (1118/1392 nt) | selA ← | selenocysteine synthase |
| RA | NC_000913 | 3,780,833 | T→C | L336P (CTG→CCG) | lldD → | L‑lactate dehydrogenase |
| RA | NC_000913 | 3,805,788 | T→C | T55A (ACG→GCG) | waaP ← | lipopolysaccharide core heptose (I) kinase |
| RA | NC_000913 | 3,877,847 | T→C | E758G (GAA→GGA) | gyrB ← | DNA gyrase subunit B |
| RA | NC_000913 | 3,924,497 | T→C | E379E (GAA→GAG) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | NC_000913 | 3,957,219 | A→G | V201A (GTA→GCA) | ilvY ← | DNA‑binding transcriptional dual regulator IlvY |
| RA | NC_000913 | 3,975,870 | A→G | Y242C (TAC→TGC) | wecE → | dTDP‑4‑dehydro‑6‑deoxy‑D‑glucose transaminase |
| RA | NC_000913 | 3,992,127 | A→G | V325V (GTA→GTG) | cyaA → | adenylate cyclase |
| RA | NC_000913 | 4,021,860 | A→G | T545T (ACA→ACG) | ubiB → | ubiquinone biosynthesis protein UbiB |
| RA | NC_000913 | 4,041,300 | T→C | H45R (CAC→CGC) | mobB ← | molybdopterin‑guanine dinucleotide biosynthesis adaptor protein |
| RA | NC_000913 | 4,070,428 | A→G | intergenic (‑27/+87) | yihR ← / ← yihS | putative aldose 1‑epimerase YihR/sulfoquinovose isomerase |
| RA | NC_000913 | 4,178,764 | G→A | L106L (CTG→CTA) | rplK → | 50S ribosomal subunit protein L11 |
| RA | NC_000913 | 4,212,959 | G→C | intergenic (+13/‑81) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,212,973 | Δ1 bp | intergenic (+27/‑67) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,288,568 | A→G | T269A (ACC→GCC) | nrfA → | cytochrome c552 nitrite reductase |
| RA | NC_000913 | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | NC_000913 | 4,302,471 | T→C | D203G (GAC→GGC) | mdtO ← | putative multidrug efflux pump subunit MdtO |
| RA | NC_000913 | 4,326,088 | T→G | intergenic (‑347/+311) | yjdN ← / ← yjdM | conserved protein YjdN/conserved protein YjdM |
| RA | NC_000913 | 4,326,141 | T→C | intergenic (‑400/+258) | yjdN ← / ← yjdM | conserved protein YjdN/conserved protein YjdM |
| RA | NC_000913 | 4,326,147 | T→C | intergenic (‑406/+252) | yjdN ← / ← yjdM | conserved protein YjdN/conserved protein YjdM |
| JC JC | NC_000913 | 4,398,934 | IS1 (+) +8 bp | coding (1523‑1530/1848 nt) | mutL → | DNA mismatch repair protein MutL |
| RA | NC_000913 | 4,417,336 | C→T | P129S (CCC→TCC) | yjfP → | carboxylesterase |
| RA | NC_000913 | 4,439,756 | A→G | N57S (AAC→AGC) | ytfK → | DUF1107 domain‑containing protein YtfK |
| RA | NC_000913 | 4,469,180 | A→G | Y519C (TAC→TGC) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | NC_000913 | 4,472,426 | (A)8→7 | coding (108/135 nt) | pyrL ← | pyrBI operon leader peptide |
| RA | NC_000913 | 4,535,542 | A→G | pseudogene (528/1017 nt) | yjhR → | KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR |
| RA | NC_000913 | 4,597,074 | (T)8→7 | intergenic (+62/+76) | lgoD → / ← opgB | L‑galactonate oxidoreductase/phosphoglycerol transferase I |
| RA | NC_000913 | 4,635,102 | G→A | A70V (GCG→GTG) | rob ← | DNA‑binding transcriptional dual regulator Rob |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423817–3424234 | 3424538–3424239 | 6–722 | 60 [59] | [59] 60 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 101 (0.670) | 67 (0.480) | 44/390 | 2.5 | 44.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 72 (0.510) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 101 (0.670) | 62 (0.440) | 43/390 | 2.6 | 42.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 72 (0.510) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 162 (1.090) | 97/414 | 0.1 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1549173 = | 128 (0.840) | 2562 (16.970) | 276/420 | 0.0 | 94.8% | coding (1773/3048 nt) | fdnG | formate dehydrogenase N subunit alpha |
| ? | NC_000913 | = 1569731 | 154 (1.020) | coding (759/1536 nt) | gadC | L‑glutamate:4‑aminobutyrate antiporter | |||||