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 | 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 | 15,191 | G→T | C381F (TGC→TTC) | tetA → | tetracycline exporter 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 | 31,028 | C→G | P35A (CCC→GCC) | trbP → | TrbP protein |
| RA | BN000925 | 36,646 | A→G | T113A (ACT→GCT) T105A (ACT→GCT) |
istA → istA → |
IS21 transposase IS21 transposase |
| 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 |
| MC JC | NC_000913 | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | NC_000913 | 263,721 | A→G | V96A (GTA→GCA) | yafW ← | antitoxin of the YkfI‑YafW toxin‑antitoxin pair |
| RA | NC_000913 | 336,746 | T→C | G274G (GGT→GGC) | yahE → | DUF2877 domain‑containing protein YahE |
| RA | NC_000913 | 475,719 | C→T | A114V (GCG→GTG) | ybaY → | PF09619 family lipoprotein YbaY |
| RA | NC_000913 | 485,773 | A→G | T5A (ACC→GCC) | acrR → | DNA‑binding transcriptional repressor AcrR |
| RA | NC_000913 | 504,319 | A→G | G126G (GGT→GGC) | fsr ← | fosmidomycin efflux pump |
| RA | NC_000913 | 525,854 | A→G | D865G (GAC→GGC) | rhsD → | protein RhsD |
| RA | NC_000913 | 731,061 | C→T | G493G (GGC→GGT) | rhsC → | rhs element protein RhsC |
| RA | NC_000913 | 736,871 | A→G | intergenic (+172/‑29) | ybfQ → / → ybfL | inactive transposase YbfQ/putative transposase YbfL |
| RA | NC_000913 | 802,681 | A→G | G265G (GGA→GGG) | ybhI → | putative tricarboxylate transporter |
| RA | NC_000913 | 883,192 | A→G | V66A (GTC→GCC) | ybjG ← | undecaprenyl pyrophosphate phosphatase |
| RA | NC_000913 | 986,795 | Δ1 bp | coding (188/1089 nt) | ompF ← | outer membrane porin F |
| RA | NC_000913 | 1,068,671 | A→G | V390A (GTA→GCA) | rutG ← | pyrimidine:H(+) symporter |
| RA | NC_000913 | 1,133,465 | A→G | T298A (ACG→GCG) | flgE → | flagellar hook protein FlgE |
| RA | NC_000913 | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | NC_000913 | 1,258,835 | Δ1 bp | coding (45/279 nt) | ychH → | stress‑induced protein |
| RA | NC_000913 | 1,296,375 | A→G | F583L (TTC→CTC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | NC_000913 | 1,298,371 | C→A | intergenic (‑250/‑227) | adhE ← / → ychE | aldehyde‑alcohol dehydrogenase/putative inner membrane protein |
| MC JC | NC_000913 | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | NC_000913 | 1,303,679 | C→T | Q261* (CAA→TAA) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | NC_000913 | 1,384,170 | A→G | R18R (AGA→AGG) | ycjX → | DUF463 domain‑containing protein YcjX |
| RA | NC_000913 | 1,630,547 | T→C | T123A (ACA→GCA) | ydfI ← | putative oxidoreductase YdfI |
| RA | NC_000913 | 1,640,644 | G→A | intergenic (‑59/+695) | essQ ← / ← cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock‑like protein CspB |
| RA | NC_000913 | 1,779,316 | T→C | intergenic (‑15/‑301) | ydiP ← / → ydiQ | putative DNA‑binding transcriptional regulator YdiP/putative electron transfer flavoprotein subunit YdiQ |
| RA | NC_000913 | 2,023,510 | T→C | R206R (CGT→CGC) | fliR → | flagellar biosynthesis protein FliR |
| RA | NC_000913 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | NC_000913 | 2,189,308 | T→C | T535A (ACC→GCC) | yehB ← | putative fimbrial usher protein YehB |
| RA | NC_000913 | 2,249,587 | A→T | F11Y (TTT→TAT) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | NC_000913 | 2,742,794 | G→A | E138K (GAA→AAA) | dgcN → | diguanylate cyclase DgcN |
| RA | NC_000913 | 2,781,961 | T→C | T256A (ACC→GCC) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | NC_000913 | 2,792,838 | T→C | V35A (GTG→GCG) | gabT → | 4‑aminobutyrate aminotransferase GabT |
| RA | NC_000913 | 2,830,095 | T→C | F95L (TTT→CTT) | gutQ → | D‑arabinose 5‑phosphate isomerase GutQ |
| RA | NC_000913 | 2,875,269 | T→C | T51A (ACC→GCC) | cysN ← | sulfate adenylyltransferase subunit 1 |
| RA | NC_000913 | 2,992,541 | (A)7→8 | coding (448/1377 nt) | ygeH → | putative transcriptional regulator YgeH |
| RA | NC_000913 | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | NC_000913 | 3,213,803 | T→C | S253P (TCT→CCT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | NC_000913 | 3,266,510 | T→C | T186A (ACC→GCC) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| RA | NC_000913 | 3,290,995 | G→A | D728N (GAT→AAT) | yraJ → | putative fimbrial usher protein YraJ |
| MC JC | NC_000913 | 3,366,751 | Δ295 bp | IS5‑mediated | yhcE–[yhcF] | yhcE, [yhcF] |
| RA | NC_000913 | 3,440,918 | T→C | T38A (ACT→GCT) | rpoA ← | RNA polymerase subunit alpha |
| RA | NC_000913 | 3,490,674 | Δ1 bp | coding (156/564 nt) | pabA ← | aminodeoxychorismate synthase subunit 2 |
| RA | NC_000913 | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | NC_000913 | 3,717,751 | C→T | L148L (CTG→TTG) | ghrB → | glyoxylate reductase |
| RA | NC_000913 | 3,834,319 | (C)5→4 | coding (219/2319 nt) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | NC_000913 | 3,914,585 | A→G | Y206H (TAT→CAT) | glmU ← | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase |
| RA | NC_000913 | 4,037,496 | A→T | intergenic (+161/‑23) | alaT → / → rrlA | tRNA‑Ala/23S ribosomal RNA |
| RA | NC_000913 | 4,137,246 | T→C | T138A (ACC→GCC) | yijF ← | conserved protein YijF |
| RA | NC_000913 | 4,165,913 | G→A | S162S (TCG→TCA) | murI → | glutamate racemase |
| RA | NC_000913 | 4,168,472 | G→A | intergenic (+25/‑169) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA |
| RA | NC_000913 | 4,168,475 | 2 bp→TG | intergenic (+28/‑165) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA |
| RA | NC_000913 | 4,212,973 | Δ1 bp | intergenic (+27/‑67) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,257,249 | A→G | E45E (GAA→GAG) | lexA → | DNA‑binding transcriptional repressor LexA |
| 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 | 4,345,819 | A→G | V503A (GTC→GCC) | fumB ← | fumarase B |
| RA | NC_000913 | 4,398,322 | A→T | H304L (CAC→CTC) | mutL → | DNA mismatch repair protein MutL |
| RA | NC_000913 | 4,606,095 | A→G | noncoding (71/87 nt) | leuV ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423857–3424233 | 3424445–3424238 | 6–589 | 14 [13] | [12] 14 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4037600–4037831 | 4040415–4039392 | 1562–2816 | 15 [13] | [13] 15 | rrlA | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 38 (0.720) +G |
20/428 | 1.6 | 56.4% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | = 4171849 | 59 (1.110) | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 1207790 = | 56 (1.050) | 21 (0.430) | 19/398 | 1.5 | 29.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 49 (0.990) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||