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 | 83,590 | G→T | 12.9% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 124,241 | C→T | 100% | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 461,007 | T→G | 100% | I707S (ATC→AGC) | lon → | Lon protease |
| RA | 543,062 | T→A | 11.6% | intergenic (+29/+199) | glxK → / ← allE | glycerate 2‑kinase 2/(S)‑ureidoglycine aminohydrolase |
| JC | 607,712 | Δ7 bp | 16.6% | intergenic (‑329/‑16) | ybdK ← / → sokE | carboxylate‑amine ligase/small RNA SokE |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 754,446 | A→G | 100% | L8P (CTC→CCC) | gltA ← | citrate synthase |
| RA | 760,485 | G→A | 100% | G594S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,352,751 | C→T | 41.9% | R293H (CGT→CAT) | sapD ← | putrescine ABC exporter ATP binding protein SapD |
| RA | 1,876,107 | G→A | 11.8% | M145I (ATG→ATA) | nimT → | 2‑nitroimidazole exporter |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,032,336 | G→C | 11.5% | intergenic (‑19/+48) | dcm ← / ← yedJ | DNA‑cytosine methyltransferase/putative HD superfamily phosphohydrolase YedJ |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,368,101 | T→C | 100% | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,623,603 | C→T | 41.7% | P187L (CCA→CTA) | ppk → | polyphosphate kinase |
| RA | 2,661,821 | C→G | 100% | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,872,022 | G→A | 29.2% | R157C (CGC→TGC) | ispD ← | 2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,473,614 | C→T | 100% | W156* (TGG→TGA) | rpsG ← | 30S ribosomal subunit protein S7 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,708,287 | C→T | 13.0% | intergenic (‑582/+329) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,253 | G→A | 54.7% | intergenic (‑154/+79) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,060 | C→T | 29.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,532,534 | G→C | 15.6% | A217G (GCC→GGC) | yjhP ← | KpLE2 phage‑like element; putative methyltransferase YjhP |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423745–3424525 | 3424525 | 1–781 | 10 [9] | [9] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315852 | NA (NA) | 25 (0.780) | 10/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1463 (44.410) | 251/262 | NT | 98.3% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 25 (0.750) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 1100121 = | 26 (0.780) | 4 (0.120) | 4/256 | NT | 14.5% | coding (482/555 nt) | ycdY | chaperone protein YcdY |
| ? | NC_000913 | 1100158 = | 22 (0.680) | coding (519/555 nt) | ycdY | chaperone protein YcdY | |||||
| * | ? | NC_000913 | 1207790 = | 1 (0.030) | 33 (1.130) | 28/232 | NT | 95.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 2 (0.070) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207795 = | 1 (0.030) | 3 (0.090) +C |
3/262 | NT | 66.8% | coding (295/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209615 = | 2 (0.060) | pseudogene (41/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 1 (0.030) | 20 (0.690) | 18/232 | NT | 93.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 2 (0.070) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1333674 = | 32 (0.960) | 3 (0.090) | 3/252 | NT | 8.8% | intergenic (+29/‑181) | topA/cysB | DNA topoisomerase 1/DNA‑binding transcriptional dual regulator CysB |
| ? | NC_000913 | 1333698 = | 32 (1.010) | intergenic (+53/‑157) | topA/cysB | DNA topoisomerase 1/DNA‑binding transcriptional dual regulator CysB | |||||
| * | ? | NC_000913 | 1436096 = | 30 (0.900) | 41 (1.240) | 39/262 | NT | 57.0% | coding (798/1134 nt) | ompN | outer membrane porin N |
| ? | NC_000913 | = 1441187 | 32 (0.970) | coding (130/267 nt) | ydbJ | DUF333 domain‑containing protein YdbJ | |||||
| * | ? | NC_000913 | 1437105 = | 84 (2.530) | 9 (0.270) | 8/262 | NT | 15.3% | intergenic (‑212/‑16) | ompN/micC | outer membrane porin N/small regulatory RNA MicC |
| ? | NC_000913 | = 1455347 | 16 (0.490) | coding (184/747 nt) | paaC | phenylacetyl‑CoA 1,2‑epoxidase, structural subunit | |||||
| * | ? | NC_000913 | 1886815 = | 22 (0.660) | 3 (0.100) | 3/242 | NT | 13.0% | intergenic (+5/+49) | yeaX/rnd | carnitine monooxygenase subunit YeaX/RNase D |
| ? | NC_000913 | 1886858 = | 20 (0.660) | intergenic (+48/+6) | yeaX/rnd | carnitine monooxygenase subunit YeaX/RNase D | |||||
| * | ? | NC_000913 | 2727891 = | NA (NA) | 5 (0.160) | 4/252 | NT | NA | noncoding (1294/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3042324 = | NA (NA) | 3 (0.090) | 3/256 | NT | NA | noncoding (3/36 nt) | other | REP210a |
| ? | NC_000913 | 3042350 = | NA (NA) | noncoding (29/36 nt) | other | REP210a | |||||
| * | ? | NC_000913 | 3094018 = | NA (NA) | 3 (0.100) | 3/250 | NT | NA | noncoding (33/36 nt) | other | REP216b |
| ? | NC_000913 | 3094050 = | NA (NA) | noncoding (1/36 nt) | other | REP216b | |||||
| * | ? | NC_000913 | = 3868326 | 45 (1.360) | 4 (0.130) | 4/250 | NT | 8.5% | coding (984/1248 nt) | yidR | DUF3748 domain‑containing galacturonate catabolism protein YidR |
| ? | NC_000913 | = 3868333 | 44 (1.400) | coding (977/1248 nt) | yidR | DUF3748 domain‑containing galacturonate catabolism protein YidR | |||||
| * | ? | NC_000913 | 4094688 = | NA (NA) | 3 (0.100) | 3/250 | NT | NA | noncoding (31/34 nt) | other | REP299i |
| ? | NC_000913 | 4094718 = | NA (NA) | noncoding (1/34 nt) | other | REP299i | |||||
| * | ? | NC_000913 | 4100553 = | 31 (0.930) | 6 (0.180) | 6/264 | NT | 17.4% | intergenic (‑28/‑257) | rhaT/sodA | rhamnose/lyxose:H(+) symporter/superoxide dismutase (Mn) |
| ? | NC_000913 | = 4102459 | 26 (0.780) | coding (770/984 nt) | kdgT | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter | |||||