mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 3,875,521 | 0 | T→C | 15.2% | 17.9 ‑10.7 ‑0.0 | 134 | A28A (GCT→GCC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,522 | 0 | C→G | 11.2% | 16.5 ‑7.9 0.0 | 134 | L29V (CTG→GTG) | yidX | putative lipoprotein |
| * | NC_000913 | 618,077 | 0 | T→G | 100.0% | 3.2 | 1 | intergenic (+39/‑177) | entF/fepE | enterobactin synthase multienzyme complex component, ATP‑dependent/regulator of length of O‑antigen component of lipopolysaccharide chains |
| * | NC_000913 | 1,168,968 | 0 | T→A | 100.0% | 2.5 | 2 | intergenic (‑136/‑105) | ycfQ/bhsA | repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein |
| * | NC_000913 | 2,192,352 | 0 | T→G | 100.0% | 1.4 | 1 | intergenic (‑130/+163) | yehD/yehE | putative fimbrial‑like adhesin protein/DUF2574 family protein |
| * | NC_000913 | 1,633,320 | 0 | T→C | 100.0% | 1.2 | 1 | intergenic (+15/‑302) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 2,192,349 | 0 | C→A | 100.0% | 0.9 | 1 | intergenic (‑127/+166) | yehD/yehE | putative fimbrial‑like adhesin protein/DUF2574 family protein |
| * | NC_000913 | 1,633,503 | 0 | G→A | 100.0% | 0.6 | 1 | intergenic (+198/‑119) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 3,805,098 | 0 | T→C | 100.0% | 0.6 | 1 | N7D (AAT→GAT) | waaS | lipopolysaccharide rhamnose:KdoIII transferase; lipopolysaccharide core biosynthesis protein |
| * | NC_000913 | 1,433,983 | 0 | T→G | 100.0% | 0.4 | 1 | intergenic (‑309/+8) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C→T | 24.2% | 106.1 ‑1.0 ‑0.1 | 165 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 25 (0.260) | 20/288 | 4.0 | 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 | = 1299498 | 0 (0.000) | 16 (0.160) | 13/296 | 6.0 | 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 | 1242577 = | 88 (0.860) | 8 (0.090) | 6/268 | 8.2 | 9.5% | coding (504/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | 1242595 = | 74 (0.820) | coding (486/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | 761823 = | 107 (1.050) | 6 (0.060) | 5/282 | 9.1 | 5.8% | coding (302/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 761890 = | 95 (1.000) | coding (369/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | = 3693567 | 260 (2.540) | 6 (0.060) | 5/288 | 9.2 | 2.4% | coding (1670/2619 nt) | bcsA | cellulose synthase, catalytic subunit |
| ? | NC_000913 | = 3693598 | 248 (2.560) | coding (1639/2619 nt) | bcsA | cellulose synthase, catalytic subunit | |||||
| * | ? | NC_000913 | = 3739543 | 191 (1.870) | 5 (0.050) | 5/284 | 9.1 | 2.7% | intergenic (+16/‑162) | malS/avtA | alpha‑amylase/valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase |
| ? | NC_000913 | = 3739556 | 184 (1.930) | intergenic (+29/‑149) | malS/avtA | alpha‑amylase/valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase | |||||
| * | ? | NC_000913 | = 3880655 | 264 (2.580) | 5 (0.050) | 5/284 | 9.1 | 2.1% | coding (567/1074 nt) | recF | gap repair protein |
| ? | NC_000913 | = 3880717 | 229 (2.400) | coding (505/1074 nt) | recF | gap repair protein | |||||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 5 (0.050) | 4/286 | 9.8 | 100% | coding (687/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619892 = | 0 (0.000) | coding (701/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 373048 = | 114 (1.110) | 4 (0.040) | 4/268 | 9.4 | 3.7% | coding (128/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding |
| ? | NC_000913 | 373066 = | 107 (1.190) | coding (146/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding | |||||
| * | ? | NC_000913 | = 3671463 | 176 (1.720) | 4 (0.040) | 4/290 | 9.9 | 2.3% | coding (432/603 nt) | yhjB | putative DNA‑binding transcriptional response regulator |
| ? | NC_000913 | = 3671507 | 178 (1.820) | coding (388/603 nt) | yhjB | putative DNA‑binding transcriptional response regulator | |||||
| * | ? | NC_000913 | = 3864141 | 199 (1.950) | 4 (0.040) | 4/288 | 9.8 | 2.0% | coding (243/717 nt) | yidP | UTRA domain‑containing GntR family putative transcriptional regulator |
| ? | NC_000913 | = 3864170 | 200 (2.060) | coding (272/717 nt) | yidP | UTRA domain‑containing GntR family putative transcriptional regulator | |||||
| * | ? | NC_000913 | = 4309625 | 125 (1.220) | 4 (0.040) | 4/288 | 9.8 | 3.3% | coding (1356/1533 nt) | alsA | D‑allose ABC transporter ATPase |
| ? | NC_000913 | = 4309649 | 114 (1.180) | coding (1332/1533 nt) | alsA | D‑allose ABC transporter ATPase | |||||
| * | ? | NC_000913 | = 414826 | 104 (1.020) | 4 (0.040) | 3/290 | 10.6 | 3.9% | coding (928/3147 nt) | sbcC | exonuclease, dsDNA, ATP‑dependent |
| ? | NC_000913 | = 414832 | 97 (0.990) | coding (922/3147 nt) | sbcC | exonuclease, dsDNA, ATP‑dependent | |||||
| * | ? | NC_000913 | 2897255 = | 94 (0.920) | 4 (0.040) | 3/288 | 10.5 | 4.3% | coding (616/1338 nt) | ygcS | putative MFS sugar transporter; membrane protein |
| ? | NC_000913 | 2897354 = | 87 (0.900) | coding (517/1338 nt) | ygcS | putative MFS sugar transporter; membrane protein | |||||
| * | ? | NC_000913 | 285874 = | 95 (0.930) | 3 (0.030) | 3/288 | 10.5 | 3.2% | coding (480/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter |
| ? | NC_000913 | 285896 = | 89 (0.920) | coding (502/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter | |||||
| * | ? | NC_000913 | = 457323 | 108 (1.060) | 3 (0.030) | 3/288 | 10.5 | 2.8% | intergenic (+23/‑103) | clpP/clpX | proteolytic subunit of ClpA‑ClpP and ClpX‑ClpP ATP‑dependent serine proteases/ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease |
| ? | NC_000913 | = 457337 | 103 (1.060) | intergenic (+37/‑89) | clpP/clpX | proteolytic subunit of ClpA‑ClpP and ClpX‑ClpP ATP‑dependent serine proteases/ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease | |||||
| * | ? | NC_000913 | 1613267 = | 101 (0.990) | 3 (0.030) | 3/286 | 10.5 | 3.1% | intergenic (‑16/+48) | glsB/sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| ? | NC_000913 | 1613289 = | 95 (0.990) | intergenic (‑38/+26) | glsB/sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent | |||||
| * | ? | NC_000913 | 1740872 = | 81 (0.790) | 3 (0.030) | 3/290 | 10.6 | 3.5% | coding (962/1212 nt) | ydhC | putative arabinose efflux transporter |
| ? | NC_000913 | 1740913 = | 90 (0.920) | coding (1003/1212 nt) | ydhC | putative arabinose efflux transporter | |||||
| * | ? | NC_000913 | 1888562 = | 92 (0.900) | 3 (0.030) | 3/286 | 10.5 | 3.3% | coding (1185/1686 nt) | fadD | acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase) |
| ? | NC_000913 | = 1888558 | 88 (0.910) | coding (1189/1686 nt) | fadD | acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase) | |||||
| * | ? | NC_000913 | 2093959 = | 108 (1.060) | 3 (0.030) | 3/292 | 10.6 | 2.8% | coding (492/1068 nt) | hisB | histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase |
| ? | NC_000913 | 2093980 = | 102 (1.040) | coding (513/1068 nt) | hisB | histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase | |||||
| * | ? | NC_000913 | = 2331858 | 96 (0.940) | 3 (0.030) | 3/288 | 10.5 | 3.2% | pseudogene (2545/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| ? | NC_000913 | = 2331859 | 93 (0.960) | pseudogene (2544/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein | |||||
| * | ? | NC_000913 | = 2962469 | 97 (0.950) | 3 (0.030) | 3/286 | 10.5 | 2.9% | coding (296/324 nt) | ppdC | putative prepilin peptidase‑dependent protein |
| ? | NC_000913 | = 2962525 | 108 (1.120) | coding (240/324 nt) | ppdC | putative prepilin peptidase‑dependent protein | |||||
| * | ? | NC_000913 | = 3076064 | 93 (0.910) | 3 (0.030) | 3/288 | 10.5 | 3.4% | coding (119/966 nt) | yggF | fructose 1,6 bisphosphatase isozyme |
| ? | NC_000913 | = 3076121 | 85 (0.880) | coding (62/966 nt) | yggF | fructose 1,6 bisphosphatase isozyme | |||||
| * | ? | NC_000913 | 3216165 = | 96 (0.940) | 4 (0.040) | 3/284 | 10.4 | 4.5% | coding (327/765 nt) | yqjH | putative siderophore interacting protein |
| ? | NC_000913 | 3216247 = | 82 (0.860) | coding (245/765 nt) | yqjH | putative siderophore interacting protein | |||||
| * | ? | NC_000913 | = 3240729 | 108 (1.060) | 3 (0.030) | 3/296 | 10.7 | 2.8% | coding (786/1245 nt) | sstT | sodium:serine/threonine symporter |
| ? | NC_000913 | 3240733 = | 105 (1.050) | coding (790/1245 nt) | sstT | sodium:serine/threonine symporter | |||||
| * | ? | NC_000913 | 3528193 = | 104 (1.020) | 3 (0.030) | 3/292 | 10.6 | 2.9% | coding (1725/2136 nt) | yrfF | putative RcsCDB‑response attenuator, inner membrane protein |
| ? | NC_000913 | 3528278 = | 98 (1.000) | coding (1810/2136 nt) | yrfF | putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 3620868 | NA (NA) | 3 (0.030) | 3/282 | 10.4 | 7.1% | coding (1677/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3621008 | 42 (0.410) | coding (1817/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3659552 = | 249 (2.430) | 3 (0.030) | 3/290 | 10.6 | 1.3% | coding (321/1158 nt) | mdtE | anaerobic multidrug efflux transporter, ArcA‑regulated |
| ? | NC_000913 | 3659580 = | 229 (2.350) | coding (349/1158 nt) | mdtE | anaerobic multidrug efflux transporter, ArcA‑regulated | |||||
| * | ? | NC_000913 | 3686335 = | 233 (2.280) | 3 (0.030) | 3/284 | 10.4 | 1.5% | coding (2839/3474 nt) | bcsC | cellulose synthase subunit |
| ? | NC_000913 | 3686435 = | 177 (1.850) | coding (2739/3474 nt) | bcsC | cellulose synthase subunit | |||||
| * | ? | NC_000913 | = 3702834 | 217 (2.120) | 3 (0.030) | 3/286 | 10.5 | 1.4% | coding (35/1005 nt) | dppF | dipeptide/heme ABC transporter ATPas |
| ? | NC_000913 | = 3702839 | 207 (2.150) | coding (30/1005 nt) | dppF | dipeptide/heme ABC transporter ATPas | |||||
| * | ? | NC_000913 | = 3760314 | 181 (1.770) | 3 (0.030) | 3/288 | 10.5 | 1.5% | coding (936/1392 nt) | selA | selenocysteine synthase |
| ? | NC_000913 | = 3760393 | 223 (2.300) | coding (857/1392 nt) | selA | selenocysteine synthase | |||||
| * | ? | NC_000913 | 3856874 = | 247 (2.410) | 3 (0.030) | 3/282 | 10.4 | 1.3% | intergenic (+10/+37) | yidI/yidJ | inner membrane protein/sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | 3856909 = | 228 (2.400) | intergenic (+45/+2) | yidI/yidJ | inner membrane protein/sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | = 3876768 | 181 (1.770) | 3 (0.030) | 3/288 | 10.5 | 1.6% | coding (185/813 nt) | yidA | sugar phosphate phosphatase |
| ? | NC_000913 | = 3876814 | 198 (2.040) | coding (139/813 nt) | yidA | sugar phosphate phosphatase | |||||
| * | ? | NC_000913 | = 4560362 | 118 (1.150) | 3 (0.030) | 3/286 | 10.5 | 2.6% | coding (319/684 nt) | yjiH | nucleoside recognition pore and gate family putative inner membrane transporter |
| ? | NC_000913 | = 4560467 | 111 (1.150) | coding (214/684 nt) | yjiH | nucleoside recognition pore and gate family putative inner membrane transporter | |||||