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 | 3,781,152 | 0 | A→G | 13.7% | 25.1 ‑41.5 ‑0.0 | 183 | intergenic (+135/‑63) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,875,521 | 0 | T→C | 17.0% | 20.9 ‑9.1 0.0 | 107 | A28A (GCT→GCC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,781,140 | 0 | A→G | 12.2% | 16.6 ‑37.9 0.0 | 183 | intergenic (+123/‑75) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,875,529 | 0 | C→G | 11.7% | 14.5 ‑5.6 0.0 | 112 | S31C (TCC→TGC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,608,682 | 0 | T→C | 11.1% | 10.1 ‑8.8 0.0 | 83 | intergenic (+33/+69) | zntA/tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| * | NC_000913 | 3,426,983 | 0 | G→T | 100.0% | 2.0 | 1 | noncoding (51/76 nt) | alaU | tRNA‑Ala |
| * | NC_000913 | 3,619,467 | 0 | C→G | 100.0% | 1.3 | 1 | L92L (CTC→CTG) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 2,997,525 | 0 | A→G | 100.0% | 0.8 | 1 | F26L (TTT→CTT) | insC1 | IS2 repressor TnpA |
| * | NC_000913 | 2,997,531 | 0 | G→T | 100.0% | 0.8 | 1 | Q24K (CAG→AAG) | insC1 | IS2 repressor TnpA |
| * | NC_000913 | 3,804,916 | 0 | A→C | 100.0% | 0.6 | 1 | D67E (GAT→GAG) | waaS | lipopolysaccharide rhamnose:KdoIII transferase; lipopolysaccharide core biosynthesis protein |
| * | NC_000913 | 1,634,433 | 0 | T→A | 100.0% | ‑0.5 | 1 | A151A (GCA→GCT) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,434 | 0 | G→A | 100.0% | ‑0.5 | 1 | A151V (GCA→GTA) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,435 | 0 | C→A | 100.0% | ‑0.5 | 1 | A151S (GCA→TCA) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,437 | 0 | G→A | 100.0% | ‑0.5 | 1 | A150V (GCT→GTT) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,438 | 0 | C→A | 100.0% | ‑0.5 | 1 | A150S (GCT→TCT) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,440 | 0 | T→A | 100.0% | ‑0.5 | 1 | D149V (GAT→GTT) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C→T | 18.1% | 73.0 ‑0.4 ‑0.2 | 155 | 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 | = 1299498 | 0 (0.000) | 24 (0.210) | 20/292 | 5.6 | 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) | 18 (0.160) | 13/284 | 7.6 | 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 | 3867985 = | 232 (1.970) | 7 (0.060) | 6/284 | 10.9 | 3.1% | coding (258/333 nt) | yidQ | DUF1375 family outer membrane protein |
| ? | NC_000913 | 3868014 = | 216 (1.930) | coding (287/333 nt) | yidQ | DUF1375 family outer membrane protein | |||||
| * | ? | NC_000913 | = 3775724 | 287 (2.430) | 6 (0.050) | 5/280 | 11.4 | 2.3% | coding (153/588 nt) | mtlR | mannitol operon repressor |
| ? | NC_000913 | = 3775808 | 238 (2.160) | coding (237/588 nt) | mtlR | mannitol operon repressor | |||||
| * | ? | NC_000913 | 307356 = | 96 (0.810) | 5 (0.040) | 5/284 | 11.5 | 5.4% | coding (1977/2526 nt) | ecpC | ECP production outer membrane protein |
| ? | NC_000913 | 307385 = | 85 (0.760) | coding (1948/2526 nt) | ecpC | ECP production outer membrane protein | |||||
| * | ? | NC_000913 | 1045201 = | 108 (0.920) | 5 (0.050) | 5/282 | 11.5 | 4.5% | coding (603/1140 nt) | gfcE | putative O‑antigen capsule outer membrane auxillary protein export channel |
| ? | NC_000913 | 1045310 = | 109 (0.980) | coding (494/1140 nt) | gfcE | putative O‑antigen capsule outer membrane auxillary protein export channel | |||||
| * | ? | NC_000913 | 3007598 = | 93 (0.790) | 5 (0.050) | 5/268 | 11.1 | 5.6% | coding (89/1197 nt) | ygeX | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| ? | NC_000913 | 3007614 = | 87 (0.830) | coding (105/1197 nt) | ygeX | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent | |||||
| * | ? | NC_000913 | = 4041215 | 92 (0.780) | 5 (0.050) | 5/280 | 11.4 | 5.4% | coding (219/528 nt) | mobB | molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913 | = 4041221 | 90 (0.820) | coding (213/528 nt) | mobB | molybdopterin‑guanine dinucleotide biosynthesis protein B | |||||
| * | ? | NC_000913 | 3927418 = | 96 (0.810) | 5 (0.050) | 4/276 | 12.0 | 5.1% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 96 (0.880) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | = 4006603 | 120 (1.020) | 5 (0.040) | 4/286 | 12.3 | 4.0% | coding (740/1830 nt) | recQ | ATP‑dependent DNA helicase |
| ? | NC_000913 | = 4006647 | 125 (1.110) | coding (784/1830 nt) | recQ | ATP‑dependent DNA helicase | |||||
| * | ? | NC_000913 | = 493333 | 79 (0.670) | 4 (0.040) | 4/284 | 12.2 | 4.9% | coding (1242/1932 nt) | dnaX | DNA polymerase III/DNA elongation factor III, tau and gamma subunits |
| ? | NC_000913 | = 493336 | 79 (0.710) | coding (1245/1932 nt) | dnaX | DNA polymerase III/DNA elongation factor III, tau and gamma subunits | |||||
| * | ? | NC_000913 | = 3693567 | 277 (2.350) | 4 (0.040) | 4/284 | 12.2 | 1.5% | coding (1670/2619 nt) | bcsA | cellulose synthase, catalytic subunit |
| ? | NC_000913 | = 3693598 | 247 (2.210) | coding (1639/2619 nt) | bcsA | cellulose synthase, catalytic subunit | |||||
| * | ? | NC_000913 | = 3739543 | 221 (1.870) | 4 (0.040) | 4/280 | 12.1 | 1.9% | intergenic (+16/‑162) | malS/avtA | alpha‑amylase/valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase |
| ? | NC_000913 | = 3739556 | 218 (1.980) | intergenic (+29/‑149) | malS/avtA | alpha‑amylase/valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase | |||||
| * | ? | NC_000913 | = 3876768 | 115 (0.970) | 4 (0.040) | 4/284 | 12.2 | 3.5% | coding (185/813 nt) | yidA | sugar phosphate phosphatase |
| ? | NC_000913 | = 3876814 | 110 (0.990) | coding (139/813 nt) | yidA | sugar phosphate phosphatase | |||||
| * | ? | NC_000913 | 4542682 = | 5 (0.040) | 4 (0.040) | 4/282 | 12.2 | 13.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 47 (0.420) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 3998038 = | 103 (0.870) | 5 (0.040) | 3/286 | 13.1 | 5.0% | coding (56/2163 nt) | uvrD | DNA‑dependent ATPase I and helicase II |
| ? | NC_000913 | 3998077 = | 91 (0.810) | coding (95/2163 nt) | uvrD | DNA‑dependent ATPase I and helicase II | |||||
| * | ? | NC_000913 | 4516891 = | 104 (0.880) | 5 (0.050) | 3/282 | 12.9 | 4.9% | coding (827/954 nt) | fecR | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| ? | NC_000913 | 4516925 = | 98 (0.880) | coding (793/954 nt) | fecR | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator | |||||
| * | ? | NC_000913 | 1143957 = | 135 (1.140) | 4 (0.040) | 3/272 | 12.7 | 3.1% | coding (411/3186 nt) | rne | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| ? | NC_000913 | 1143971 = | 129 (1.210) | coding (397/3186 nt) | rne | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein | |||||
| * | ? | NC_000913 | 3858193 = | 232 (1.970) | 4 (0.040) | 3/274 | 12.7 | 1.9% | coding (212/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | 3858242 = | 208 (1.930) | coding (163/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | 4255890 = | 138 (1.170) | 4 (0.040) | 3/284 | 13.0 | 2.9% | coding (577/2424 nt) | plsB | glycerol‑3‑phosphate O‑acyltransferase |
| ? | NC_000913 | 4256077 = | 139 (1.240) | coding (390/2424 nt) | plsB | glycerol‑3‑phosphate O‑acyltransferase | |||||
| * | ? | NC_000913 | = 525155 | 106 (0.900) | 3 (0.030) | 3/286 | 13.1 | 2.9% | coding (1895/4281 nt) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3621044 | NA (NA) | coding (1853/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 732856 = | 113 (0.960) | 3 (0.030) | 3/286 | 13.1 | 2.7% | coding (3274/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3622440 = | NA (NA) | coding (3249/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 1285349 | 110 (0.930) | 3 (0.030) | 3/284 | 13.0 | 2.7% | coding (211/711 nt) | narJ | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 |
| ? | NC_000913 | = 1285396 | 111 (0.990) | coding (258/711 nt) | narJ | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 | |||||
| * | ? | NC_000913 | = 1428843 | NA (NA) | 3 (0.030) | 3/284 | 13.0 | 2.7% | pseudogene (48/189 nt) | lomR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion |
| ? | NC_000913 | = 1428931 | 108 (0.970) | pseudogene (136/189 nt) | lomR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion | |||||
| * | ? | NC_000913 | 1739638 = | 90 (0.760) | 3 (0.030) | 3/284 | 13.0 | 3.4% | coding (161/933 nt) | ydhB | LysR family putative transcriptional regulator |
| ? | NC_000913 | 1739666 = | 84 (0.750) | coding (133/933 nt) | ydhB | LysR family putative transcriptional regulator | |||||
| * | ? | NC_000913 | 1997022 = | 73 (0.620) | 3 (0.030) | 3/280 | 12.9 | 4.0% | intergenic (‑190/+40) | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC transporter ATPase |
| ? | NC_000913 | 1997051 = | 77 (0.700) | intergenic (‑219/+11) | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC transporter ATPase | |||||
| * | ? | NC_000913 | = 2318722 | 97 (0.820) | 3 (0.030) | 3/284 | 13.0 | 2.8% | coding (1155/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| ? | NC_000913 | = 2318773 | 116 (1.040) | coding (1104/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN | |||||
| * | ? | NC_000913 | = 2319247 | 130 (1.100) | 3 (0.030) | 3/284 | 13.0 | 2.4% | coding (630/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| ? | NC_000913 | = 2319264 | 125 (1.120) | coding (613/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN | |||||
| * | ? | NC_000913 | = 2331858 | 121 (1.030) | 3 (0.030) | 3/284 | 13.0 | 2.5% | pseudogene (2545/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| ? | NC_000913 | = 2331859 | 116 (1.040) | pseudogene (2544/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein | |||||
| * | ? | NC_000913 | = 2593882 | 134 (1.140) | 3 (0.030) | 3/286 | 13.1 | 2.3% | coding (1978/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase |
| ? | NC_000913 | = 2593918 | 126 (1.120) | coding (1942/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase | |||||
| * | ? | NC_000913 | = 3381847 | 114 (0.970) | 3 (0.030) | 3/282 | 12.9 | 2.7% | coding (1105/1368 nt) | degQ | serine endoprotease, periplasmic |
| ? | NC_000913 | = 3381859 | 106 (0.960) | coding (1117/1368 nt) | degQ | serine endoprotease, periplasmic | |||||
| * | ? | NC_000913 | = 3621044 | NA (NA) | 4 (0.040) | 3/286 | 13.1 | 4.6% | coding (1853/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3621074 | 87 (0.740) | coding (1883/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 3781125 | 184 (1.560) | 3 (0.030) | 3/290 | 13.2 | 1.7% | intergenic (+108/‑90) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| ? | NC_000913 | = 3781138 | 179 (1.570) | intergenic (+121/‑77) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 3858205 | 230 (1.950) | 3 (0.030) | 3/274 | 12.7 | 1.4% | coding (200/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | = 3858228 | 208 (1.930) | coding (177/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | = 3894310 | 133 (1.130) | 3 (0.030) | 3/284 | 13.0 | 2.3% | coding (430/750 nt) | yieE | phosphopantetheinyl transferase superfamily protein |
| ? | NC_000913 | = 3894317 | 129 (1.160) | coding (437/750 nt) | yieE | phosphopantetheinyl transferase superfamily protein | |||||
| * | ? | NC_000913 | = 3895233 | 122 (1.030) | 3 (0.030) | 3/276 | 12.8 | 2.6% | intergenic (+15/+39) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter |
| ? | NC_000913 | = 3895244 | 116 (1.070) | intergenic (+26/+28) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter | |||||
| * | ? | NC_000913 | 4289016 = | 142 (1.200) | 3 (0.030) | 3/282 | 12.9 | 2.2% | coding (1253/1437 nt) | nrfA | nitrite reductase, formate‑dependent, cytochrome |
| ? | NC_000913 | 4289092 = | 138 (1.240) | coding (1329/1437 nt) | nrfA | nitrite reductase, formate‑dependent, cytochrome | |||||