mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 82,766 | A→G | 12.3% | L255P (CTC→CCC) | leuA ← | 2‑isopropylmalate synthase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 349,717 | T→C | 5.9% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 353,610 | C→G | 12.5% | A302G (GCG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | 357,775 | A→T | 7.3% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 357,778 | C→T | 8.4% | intergenic (+324/+13) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 375,247 | A→G | 8.9% | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 422,247 | A→T | 9.0% | Y421F (TAT→TTT) | proY → | proline‑specific permease |
| RA | 514,757 | T→C | 15.7% | S35G (AGC→GGC) | ybbJ ← | inner membrane protein; stimulator of the QmcA suppressor of ftsH‑htpX |
| RA | 738,514 | A→G | 7.2% | G141G (GGA→GGG) | ybfD → | H repeat‑associated putative transposase |
| RA | 811,721 | T→G | 23.0% | V67G (GTG→GGG) | bioC → | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| RA | 1,258,996 | T→G | 15.9% | V69G (GTG→GGG) | ychH → | DUF2583 family putative inner membrane protein |
| RA | 1,269,362 | G→T | 6.8% | noncoding (40/67 nt) | rdlA → | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,460,743 | A→G | 7.0% | G91G (GGA→GGG) | paaI → | hydroxyphenylacetyl‑CoA thioesterase |
| RA | 1,466,856 | A→G | 7.2% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,529,304 | A→C | 9.3% | pseudogene (1403/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,828,890 | C→A | 6.2% | R282L (CGT→CTT) | astD ← | succinylglutamic semialdehyde dehydrogenase |
| RA | 1,856,134 | A→C | 10.4% | G265G (GGT→GGG) | ydjH ← | putative kinase |
| RA | 1,921,544 | T→G | 17.6% | V441G (GTA→GGA) | rsmF → | 16S rRNA m(5)C1407 methyltransferase, SAM‑dependent |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,151,689 | G→T | 35.9% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| 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 | 2,248,431 | A→C | 12.2% | G34G (GGT→GGG) | lysP ← | lysine transporter |
| RA | 2,304,988 | T→C | 9.4% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,610,873 | A→C | 8.2% | T56T (ACA→ACC) | hyfI → | hydrogenase 4, Fe‑S subunit |
| RA | 2,745,089 | A→C | 28.3% | V84G (GTG→GGG) | trmD ← | tRNA m(1)G37 methyltransferase, SAM‑dependent |
| RA | 2,928,196 | G→A | 18.0% | intergenic (+524/‑33) | ygdH → / → sdaC | UPF0717 family protein/putative serine transporter |
| RA | 3,206,438 | G→A | 14.4% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,297,688 | T→C | 10.0% | M151V (ATG→GTG) | yraQ ← | putative inner membrane permease |
| RA | 3,520,796 | G→T | 10.7% | T75K (ACA→AAA) | hofP ← | DNA catabolic protein |
| 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 |
| RA | 3,760,384 | A→C | 18.2% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,661 | T→G | 33.8% | pseudogene (943/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,862,674 | C→A | 31.0% | pseudogene (930/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,862,677 | G→C | 31.6% | pseudogene (927/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,875,536 | C→A | 9.4% | T33T (ACC→ACA) | yidX → | putative lipoprotein |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,153,472 | C→A | 5.0% | intergenic (‑374/+224) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 20.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 21.9% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 9.7% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 10.2% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +C | 94.7% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:2 | +G | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,397 | T→C | 5.2% | intergenic (+603/+39) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,247 | C→T | 5.9% | intergenic (‑506/+152) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,614,496 | C→T | 5.2% | intergenic (+236/+184) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,626,668 | A→C | 10.9% | T253P (ACC→CCC) | radA → | DNA repair protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423815–3424234 | 3424458–3424238 | 5–644 | 42 [40] | [37] 41 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 274456 | NA (NA) | 3 (0.020) | 3/318 | NT | NA | noncoding (694/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274878 | NA (NA) | noncoding (272/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 6 (0.040) | 5/318 | NT | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 523984 = | 45 (0.310) | 4 (0.030) | 4/320 | NT | 6.9% | coding (724/4281 nt) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 524076 = | 65 (0.480) | coding (816/4281 nt) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 1207790 = | 59 (0.410) | 93 (0.720) | 62/304 | NT | 65.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 46 (0.360) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 61 (0.430) | 63 (0.490) | 45/304 | NT | 55.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 46 (0.360) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 110 (0.790) | 67/328 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 117 (0.860) | 76/320 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 2286126 = | 120 (0.840) | 6 (0.050) | 6/310 | NT | 5.7% | coding (1751/1761 nt) | yejM | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor |
| ? | NC_000913 | 2286159 = | 89 (0.670) | intergenic (+23/‑52) | yejM/proL | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro | |||||
| * | ? | NC_000913 | 2355925 = | 112 (0.780) | 6 (0.040) | 3/324 | NT | 5.3% | coding (405/1191 nt) | glpC | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster |
| ? | NC_000913 | 2355977 = | 105 (0.760) | coding (457/1191 nt) | glpC | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster | |||||
| * | ? | NC_000913 | = 2375831 | 57 (0.410) | 6 (0.040) | 6/328 | NT | 9.5% | coding (132/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | = 2515617 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 2594348 = | 110 (0.770) | 5 (0.040) | 5/314 | NT | 5.1% | coding (1512/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase |
| ? | NC_000913 | 2594774 = | 84 (0.630) | coding (1086/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase | |||||
| * | ? | NC_000913 | 2625196 = | 105 (0.730) | 8 (0.060) | 3/330 | NT | 6.8% | coding (82/1542 nt) | ppx | exopolyphosphatase |
| ? | NC_000913 | 2625297 = | 116 (0.830) | coding (183/1542 nt) | ppx | exopolyphosphatase | |||||
| * | ? | NC_000913 | = 2730267 | NA (NA) | 8 (0.060) | 6/324 | NT | NA | noncoding (891/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 2730343 | NA (NA) | noncoding (815/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | 2796243 = | 94 (0.660) | 6 (0.040) | 6/318 | NT | 6.1% | coding (570/663 nt) | csiR | transcriptional repressor of csiD |
| ? | NC_000913 | 2796271 = | 95 (0.700) | coding (598/663 nt) | csiR | transcriptional repressor of csiD | |||||
| * | ? | NC_000913 | 2972714 = | 124 (0.870) | 6 (0.040) | 5/318 | NT | 5.2% | coding (1149/1194 nt) | lplT | lysophospholipid transporter |
| ? | NC_000913 | 2972811 = | 101 (0.750) | coding (1052/1194 nt) | lplT | lysophospholipid transporter | |||||
| * | ? | NC_000913 | = 3554077 | 91 (0.640) | 7 (0.050) | 6/330 | NT | 7.1% | coding (993/2706 nt) | malT | mal regulon transcriptional activator |
| ? | NC_000913 | = 3554095 | 93 (0.660) | coding (1011/2706 nt) | malT | mal regulon transcriptional activator | |||||
| * | ? | NC_000913 | = 3856516 | 138 (0.960) | 7 (0.050) | 4/322 | NT | 5.4% | coding (102/450 nt) | yidI | inner membrane protein |
| ? | NC_000913 | = 3856614 | 111 (0.810) | coding (200/450 nt) | yidI | inner membrane protein | |||||
| * | ? | NC_000913 | = 4498381 | 1 (0.010) | 7 (0.050) | 4/330 | NT | 87.7% | noncoding (201/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4498773 | NA (NA) | noncoding (593/1331 nt) | IS2 | repeat region | |||||