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 | 3,875,522 | 0 | C→G | 26.9% | 28.8 ‑11.2 0.0 | 67 | L29V (CTG→GTG) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,521 | 0 | T→C | 28.8% | 24.5 ‑11.4 0.0 | 67 | A28A (GCT→GCC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,529 | 0 | C→G | 23.5% | 22.1 ‑9.6 0.0 | 68 | S31C (TCC→TGC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,524 | 0 | G→C | 22.1% | 19.5 ‑8.3 0.0 | 68 | L29L (CTG→CTC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,532 | 0 | A→T | 20.6% | 10.3 ‑8.5 0.0 | 68 | H32L (CAT→CTT) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,525 | 0 | G→T | 19.1% | 10.2 ‑6.9 ‑0.0 | 68 | V30F (GTT→TTT) | yidX | putative lipoprotein |
| * | NC_000913 | 1,095,310 | 0 | T→G | 100.0% | 0.8 | 1 | E43A (GAA→GCA) | insE1 | IS3 transposase A |
| * | NC_000913 | 3,470,516 | 0 | C→T | 100.0% | ‑0.2 | 1 | G272S (GGT→AGT) | tufA | translation elongation factor EF‑Tu 1 |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C→T | 15.6% | 55.8 ‑1.4 ‑0.3 | 141 | 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 | 3927418 = | 89 (0.870) | 7 (0.070) | 7/282 | 9.5 | 7.5% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 91 (0.960) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 7 (0.070) | 6/288 | 10.2 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4409174 = | NA (NA) | 6 (0.060) | 6/276 | 9.9 | 5.4% | noncoding (22/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4409235 = | 105 (1.130) | noncoding (83/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 724120 = | 87 (0.850) | 6 (0.060) | 5/288 | 10.8 | 6.8% | coding (295/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| ? | NC_000913 | 724157 = | 82 (0.850) | coding (258/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein | |||||
| * | ? | NC_000913 | 1071360 = | 102 (0.990) | 6 (0.060) | 5/292 | 10.9 | 5.4% | coding (406/801 nt) | rutD | putative reactive intermediate detoxifying aminoacrylate hydrolase |
| ? | NC_000913 | 1071403 = | 111 (1.130) | coding (363/801 nt) | rutD | putative reactive intermediate detoxifying aminoacrylate hydrolase | |||||
| * | ? | NC_000913 | 1508853 = | 107 (1.040) | 6 (0.060) | 5/284 | 10.7 | 5.8% | coding (212/231 nt) | yncJ | uncharacterized protein |
| ? | NC_000913 | 1508894 = | 97 (1.020) | coding (171/231 nt) | yncJ | uncharacterized protein | |||||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 5 (0.050) | 5/288 | 10.8 | 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 | 3327193 = | 105 (1.020) | 5 (0.050) | 4/288 | 11.5 | 4.7% | coding (472/630 nt) | rlmE | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| ? | NC_000913 | 3327230 = | 104 (1.080) | coding (435/630 nt) | rlmE | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 373065 | 95 (0.920) | 4 (0.040) | 4/270 | 11.0 | 4.6% | coding (145/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding |
| ? | NC_000913 | = 373047 | 83 (0.920) | coding (127/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding | |||||
| * | ? | NC_000913 | = 447227 | 109 (1.060) | 5 (0.050) | 4/284 | 11.4 | 4.8% | coding (479/891 nt) | cyoE | protoheme IX farnesyltransferase |
| ? | NC_000913 | = 447266 | 98 (1.030) | coding (440/891 nt) | cyoE | protoheme IX farnesyltransferase | |||||
| * | ? | NC_000913 | 1426168 = | 109 (1.060) | 4 (0.040) | 4/286 | 11.5 | 3.6% | intergenic (+86/‑286) | ydaY/tmpR | pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein |
| ? | NC_000913 | 1426189 = | 113 (1.180) | intergenic (+107/‑265) | ydaY/tmpR | pseudogene, Rac prophage;Phage or Prophage Related/Rac prophage; pseudogene, tail protein family;Phage or Prophage Related; putative alpha helix protein | |||||
| * | ? | NC_000913 | 2197764 = | 124 (1.210) | 4 (0.040) | 4/284 | 11.4 | 3.4% | pseudogene (1291/2847 nt) | yehH | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function |
| ? | NC_000913 | 2197796 = | 112 (1.170) | pseudogene (1323/2847 nt) | yehH | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function | |||||
| * | ? | NC_000913 | = 2595154 | 84 (0.820) | 4 (0.040) | 4/286 | 11.5 | 4.9% | coding (706/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase |
| ? | NC_000913 | = 2595179 | 78 (0.810) | coding (681/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase | |||||
| * | ? | NC_000913 | = 2603770 | 83 (0.810) | 4 (0.040) | 4/290 | 11.6 | 4.5% | coding (1953/2019 nt) | hyfB | hydrogenase 4, membrane subunit |
| ? | NC_000913 | = 2603794 | 92 (0.940) | coding (1977/2019 nt) | hyfB | hydrogenase 4, membrane subunit | |||||
| * | ? | NC_000913 | 3764005 = | 35 (0.340) | 6 (0.060) | 4/290 | 11.6 | 12.2% | coding (1823/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3764057 = | 53 (0.540) | coding (1875/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3998038 = | 95 (0.920) | 4 (0.040) | 4/292 | 11.6 | 4.2% | coding (56/2163 nt) | uvrD | DNA‑dependent ATPase I and helicase II |
| ? | NC_000913 | 3998077 = | 90 (0.920) | coding (95/2163 nt) | uvrD | DNA‑dependent ATPase I and helicase II | |||||
| * | ? | NC_000913 | 730283 = | 43 (0.420) | 5 (0.050) | 3/288 | 12.3 | 11.0% | coding (701/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619878 = | NA (NA) | coding (687/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 761823 = | 87 (0.850) | 3 (0.030) | 3/284 | 12.2 | 3.7% | coding (302/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 761890 = | 76 (0.800) | coding (369/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | = 825471 | 103 (1.000) | 3 (0.030) | 3/292 | 12.4 | 3.1% | coding (638/1107 nt) | ybhR | putative ABC transporter permease |
| ? | NC_000913 | 825562 = | 91 (0.930) | coding (547/1107 nt) | ybhR | putative ABC transporter permease | |||||
| * | ? | NC_000913 | = 839933 | 82 (0.800) | 3 (0.030) | 3/290 | 12.3 | 4.0% | coding (1599/2283 nt) | fiu | catecholate siderophore receptor |
| ? | NC_000913 | = 839949 | 65 (0.670) | coding (1583/2283 nt) | fiu | catecholate siderophore receptor | |||||
| * | ? | NC_000913 | = 1373284 | 84 (0.820) | 3 (0.030) | 3/290 | 12.3 | 3.8% | coding (63/882 nt) | ycjO | putative sugar ABC transporter permease |
| ? | NC_000913 | = 1373292 | 74 (0.760) | coding (71/882 nt) | ycjO | putative sugar ABC transporter permease | |||||
| * | ? | NC_000913 | 1840631 = | 80 (0.780) | 3 (0.030) | 3/292 | 12.4 | 3.5% | coding (1165/1308 nt) | ynjE | molybdopterin synthase sulfurtransferase |
| ? | NC_000913 | 1840668 = | 89 (0.910) | coding (1202/1308 nt) | ynjE | molybdopterin synthase sulfurtransferase | |||||
| * | ? | NC_000913 | = 1950954 | 87 (0.850) | 3 (0.030) | 3/292 | 12.4 | 3.4% | coding (123/567 nt) | yecD | isochorismatase family protein |
| ? | NC_000913 | = 1950965 | 85 (0.870) | coding (134/567 nt) | yecD | isochorismatase family protein | |||||
| * | ? | NC_000913 | 1997022 = | 50 (0.490) | 3 (0.030) | 3/286 | 12.2 | 5.6% | intergenic (‑190/+40) | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC transporter ATPase |
| ? | NC_000913 | 1997051 = | 55 (0.570) | intergenic (‑219/+11) | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC transporter ATPase | |||||
| * | ? | NC_000913 | 2021646 = | 72 (0.700) | 3 (0.030) | 3/288 | 12.3 | 4.0% | coding (143/366 nt) | fliO | flagellar biosynthesis protein |
| ? | NC_000913 | 2021683 = | 78 (0.810) | coding (180/366 nt) | fliO | flagellar biosynthesis protein | |||||
| * | ? | NC_000913 | = 2408797 | NA (NA) | 3 (0.030) | 3/290 | 12.3 | NA | noncoding (6/19 nt) | REP167 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP167 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 2408804 | NA (NA) | noncoding (13/19 nt) | REP167 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP167 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | 2504705 = | 104 (1.010) | 3 (0.030) | 3/290 | 12.3 | 2.9% | coding (843/1038 nt) | ypdE | aminopeptidase |
| ? | NC_000913 | 2504736 = | 104 (1.070) | coding (812/1038 nt) | ypdE | aminopeptidase | |||||
| * | ? | NC_000913 | 2706126 = | 106 (1.030) | 3 (0.030) | 3/290 | 12.3 | 3.2% | coding (999/1800 nt) | lepA | back‑translocating elongation factor EF4, GTPase |
| ? | NC_000913 | 2706190 = | 83 (0.850) | coding (935/1800 nt) | lepA | back‑translocating elongation factor EF4, GTPase | |||||
| * | ? | NC_000913 | 3018119 = | 107 (1.040) | 3 (0.030) | 3/296 | 12.5 | 2.8% | coding (2060/3099 nt) | ygfK | putative Fe‑S subunit oxidoreductase subunit |
| ? | NC_000913 | 3018155 = | 108 (1.090) | coding (2096/3099 nt) | ygfK | putative Fe‑S subunit oxidoreductase subunit | |||||
| * | ? | NC_000913 | 3221854 = | 90 (0.880) | 3 (0.030) | 3/290 | 12.3 | 3.4% | coding (389/984 nt) | ebgR | transcriptional repressor |
| ? | NC_000913 | 3221915 = | 84 (0.860) | coding (450/984 nt) | ebgR | transcriptional repressor | |||||
| * | ? | NC_000913 | 3383284 = | 114 (1.110) | 3 (0.030) | 3/282 | 12.1 | 2.7% | intergenic (+17/+46) | degS/mdh | serine endoprotease, periplasmic/malate dehydrogenase, NAD(P)‑binding |
| ? | NC_000913 | 3383314 = | 110 (1.160) | intergenic (+47/+16) | degS/mdh | serine endoprotease, periplasmic/malate dehydrogenase, NAD(P)‑binding | |||||
| * | ? | NC_000913 | = 3579387 | 106 (1.030) | 3 (0.030) | 3/286 | 12.2 | 3.1% | coding (259/696 nt) | yhhW | quercetinase activity in vitro |
| ? | NC_000913 | = 3579470 | 86 (0.900) | coding (176/696 nt) | yhhW | quercetinase activity in vitro | |||||
| * | ? | NC_000913 | 3967692 = | 106 (1.030) | 3 (0.030) | 3/282 | 12.1 | 3.0% | intergenic (+16/‑224) | rho/wecA | transcription termination factor/UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| ? | NC_000913 | 3967720 = | 98 (1.030) | intergenic (+44/‑196) | rho/wecA | transcription termination factor/UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase | |||||
| * | ? | NC_000913 | = 4028177 | 88 (0.860) | 3 (0.030) | 3/298 | 12.6 | 3.4% | coding (596/1164 nt) | fadA | 3‑ketoacyl‑CoA thiolase (thiolase I) |
| ? | NC_000913 | = 4028231 | 84 (0.840) | coding (542/1164 nt) | fadA | 3‑ketoacyl‑CoA thiolase (thiolase I) | |||||
| * | ? | NC_000913 | = 4289024 | 125 (1.220) | 3 (0.030) | 3/288 | 12.3 | 2.3% | coding (1261/1437 nt) | nrfA | nitrite reductase, formate‑dependent, cytochrome |
| ? | NC_000913 | = 4289082 | 139 (1.440) | coding (1319/1437 nt) | nrfA | nitrite reductase, formate‑dependent, cytochrome | |||||
| * | ? | NC_000913 | = 4524799 | 109 (1.060) | 3 (0.030) | 3/286 | 12.2 | 3.2% | coding (212/906 nt) | yjhH | putative lyase/synthase |
| ? | NC_000913 | = 4524824 | 81 (0.840) | coding (187/906 nt) | yjhH | putative lyase/synthase | |||||