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 | 3,608,703 | 0 | A→G | 22.1% | 12.3 ‑14.2 ‑0.0 | 72 | intergenic (+54/+48) | zntA/tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| * | NC_000913 | 1,300,651 | 0 | C→A | 100.0% | 1.3 | 1 | intergenic (+1406/‑531) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,300,652 | 0 | T→G | 100.0% | 1.2 | 1 | intergenic (+1407/‑530) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,433,824 | 0 | T→G | 100.0% | 1.2 | 1 | intergenic (‑150/+167) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage |
| * | NC_000913 | 1,433,832 | 0 | A→T | 100.0% | 0.7 | 1 | intergenic (‑158/+159) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage |
| * | NC_000913 | 1,300,656 | 0 | T→G | 100.0% | 0.6 | 1 | intergenic (+1411/‑526) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,037,592 | 0 | A→C | 100.0% | 0.6 | 1 | noncoding (74/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon |
| * | NC_000913 | 225,377 | 0 | C→T | 100.0% | ‑0.1 | 1 | intergenic (+65/‑4) | rrsH/ileV | 16S ribosomal RNA of rrnH operon/tRNA‑Ile |
| * | NC_000913 | 4,507,942 | 0 | C→A | 100.0% | ‑0.1 | 1 | D226Y (GAT→TAT) | insI1 | IS30 transposase |
| * | NC_000913 | 4,507,954 | 0 | A→C | 100.0% | ‑0.1 | 1 | S222A (TCC→GCC) | insI1 | IS30 transposase |
| * | NC_000913 | 4,507,955 | 0 | A→G | 100.0% | ‑0.1 | 1 | R221R (CGT→CGC) | insI1 | IS30 transposase |
| * | NC_000913 | 4,507,958 | 0 | T→C | 100.0% | ‑0.1 | 1 | E220E (GAA→GAG) | insI1 | IS30 transposase |
| * | NC_000913 | 4,507,967 | 0 | T→G | 100.0% | ‑0.1 | 1 | P217P (CCA→CCC) | insI1 | IS30 transposase |
| * | NC_000913 | 225,375 | 0 | C→T | 100.0% | ‑0.2 | 1 | intergenic (+63/‑6) | rrsH/ileV | 16S ribosomal RNA of rrnH operon/tRNA‑Ile |
| * | NC_000913 | 225,376 | 0 | T→C | 100.0% | ‑0.2 | 1 | intergenic (+64/‑5) | rrsH/ileV | 16S ribosomal RNA of rrnH operon/tRNA‑Ile |
| * | NC_000913 | 225,383 | 0 | G→C | 100.0% | ‑0.2 | 1 | noncoding (3/77 nt) | ileV | tRNA‑Ile |
| * | NC_000913 | 225,387 | 0 | G→. | 100.0% | ‑0.2 | 1 | noncoding (7/77 nt) | ileV | tRNA‑Ile |
| * | NC_000913 | 225,389 | 0 | A→T | 100.0% | ‑0.2 | 1 | noncoding (9/77 nt) | ileV | tRNA‑Ile |
| * | NC_000913 | 4,507,935 | 0 | C→G | 100.0% | ‑0.2 | 1 | R228T (AGA→ACA) | insI1 | IS30 transposase |
| * | NC_000913 | 4,507,938 | 0 | T→A | 100.0% | ‑0.2 | 1 | N227I (AAC→ATC) | insI1 | IS30 transposase |
| * | NC_000913 | 4,507,940 | 0 | A→C | 100.0% | ‑0.2 | 1 | D226E (GAT→GAG) | insI1 | IS30 transposase |
| * | NC_000913 | 4,507,953 | 0 | G→A | 100.0% | ‑0.2 | 1 | S222F (TCC→TTC) | insI1 | IS30 transposase |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C→T | 16.6% | 55.5 ‑1.0 ‑0.0 | 139 | 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) | 30 (0.280) | 26/290 | 3.9 | 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 | 3221854 = | 89 (0.790) | 7 (0.070) | 7/290 | 10.0 | 8.0% | coding (389/984 nt) | ebgR | transcriptional repressor |
| ? | NC_000913 | 3221915 = | 76 (0.710) | coding (450/984 nt) | ebgR | transcriptional repressor | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 8 (0.080) | 6/288 | 10.5 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2713829 | 98 (0.870) | 6 (0.060) | 6/284 | 10.4 | 5.5% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713908 | 114 (1.090) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | = 105258 | 103 (0.920) | 6 (0.060) | 5/290 | 11.2 | 5.9% | intergenic (+14/‑47) | ftsA/ftsZ | ATP‑binding cell division FtsK recruitment protein/GTP‑binding tubulin‑like cell division protein |
| ? | NC_000913 | = 105268 | 95 (0.890) | intergenic (+24/‑37) | ftsA/ftsZ | ATP‑binding cell division FtsK recruitment protein/GTP‑binding tubulin‑like cell division protein | |||||
| * | ? | NC_000913 | 3927418 = | 127 (1.130) | 6 (0.060) | 5/282 | 11.0 | 4.8% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 122 (1.180) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | 761823 = | 90 (0.800) | 5 (0.050) | 5/284 | 11.0 | 5.4% | coding (302/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 761890 = | 92 (0.880) | coding (369/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | 3216165 = | 113 (1.000) | 5 (0.050) | 5/286 | 11.1 | 4.5% | coding (327/765 nt) | yqjH | putative siderophore interacting protein |
| ? | NC_000913 | 3216247 = | 106 (1.010) | coding (245/765 nt) | yqjH | putative siderophore interacting protein | |||||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 5 (0.050) | 5/288 | 11.1 | 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 | 4409174 = | NA (NA) | 5 (0.050) | 5/276 | 10.8 | 4.0% | 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 = | 120 (1.180) | 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 | 3037860 = | 100 (0.890) | 5 (0.050) | 4/284 | 11.7 | 4.8% | coding (247/1734 nt) | recJ | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| ? | NC_000913 | 3037943 = | 106 (1.020) | coding (164/1734 nt) | recJ | ssDNA exonuclease, 5' ‑‑> 3'‑specific | |||||
| * | ? | NC_000913 | 3381839 = | 118 (1.050) | 5 (0.050) | 4/288 | 11.8 | 4.0% | coding (1097/1368 nt) | degQ | serine endoprotease, periplasmic |
| ? | NC_000913 | 3381869 = | 129 (1.220) | coding (1127/1368 nt) | degQ | serine endoprotease, periplasmic | |||||
| * | ? | NC_000913 | = 510830 | 128 (1.140) | 4 (0.040) | 4/288 | 11.8 | 3.4% | coding (550/2505 nt) | copA | copper transporter |
| ? | NC_000913 | = 510890 | 106 (1.000) | coding (490/2505 nt) | copA | copper transporter | |||||
| * | ? | NC_000913 | = 1167401 | NA (NA) | 4 (0.040) | 4/290 | 11.9 | NA | intergenic (+12/‑198) | ndh/ycfJ | respiratory NADH dehydrogenase 2/cupric reductase/uncharacterized protein |
| ? | NC_000913 | = 1167431 | NA (NA) | noncoding (30/30 nt) | REP103 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP103 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | 2012857 = | 86 (0.760) | 4 (0.040) | 4/286 | 11.8 | 4.7% | coding (158/315 nt) | fliE | flagellar basal‑body component |
| ? | NC_000913 | 2012911 = | 83 (0.790) | coding (104/315 nt) | fliE | flagellar basal‑body component | |||||
| * | ? | NC_000913 | 2937424 = | NA (NA) | 4 (0.040) | 4/284 | 11.7 | NA | intergenic (+65/‑44) | fucI/fucK | L‑fucose isomerase/L‑fuculokinase |
| ? | NC_000913 | 2937452 = | NA (NA) | intergenic (+93/‑16) | fucI/fucK | L‑fucose isomerase/L‑fuculokinase | |||||
| * | ? | NC_000913 | = 3739543 | 109 (0.970) | 4 (0.040) | 4/286 | 11.8 | 3.8% | intergenic (+16/‑162) | malS/avtA | alpha‑amylase/valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase |
| ? | NC_000913 | = 3739556 | 103 (0.980) | intergenic (+29/‑149) | malS/avtA | alpha‑amylase/valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase | |||||
| * | ? | NC_000913 | 3858193 = | 129 (1.150) | 4 (0.040) | 4/280 | 11.6 | 3.4% | coding (212/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | 3858242 = | 106 (1.030) | coding (163/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | 3998038 = | 107 (0.950) | 4 (0.040) | 4/292 | 11.9 | 3.9% | coding (56/2163 nt) | uvrD | DNA‑dependent ATPase I and helicase II |
| ? | NC_000913 | 3998077 = | 94 (0.880) | coding (95/2163 nt) | uvrD | DNA‑dependent ATPase I and helicase II | |||||
| * | ? | NC_000913 | 190773 = | 135 (1.200) | 3 (0.030) | 3/290 | 12.6 | 2.3% | intergenic (+174/‑84) | rpsB/tsf | 30S ribosomal subunit protein S2/translation elongation factor EF‑Ts |
| ? | NC_000913 | 190796 = | 132 (1.240) | intergenic (+197/‑61) | rpsB/tsf | 30S ribosomal subunit protein S2/translation elongation factor EF‑Ts | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 3 (0.030) | 3/292 | 12.7 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 251816 | 108 (0.960) | 3 (0.030) | 3/290 | 12.6 | 3.0% | coding (919/1056 nt) | dinB | DNA polymerase IV |
| ? | NC_000913 | = 251864 | 95 (0.890) | coding (967/1056 nt) | dinB | DNA polymerase IV | |||||
| * | ? | NC_000913 | = 632346 | 126 (1.120) | 3 (0.030) | 3/292 | 12.7 | 2.5% | coding (165/198 nt) | ybdD | DUF466 family protein |
| ? | NC_000913 | = 632362 | 114 (1.060) | coding (181/198 nt) | ybdD | DUF466 family protein | |||||
| * | ? | NC_000913 | = 682737 | 121 (1.080) | 3 (0.030) | 3/288 | 12.6 | 2.6% | coding (657/1671 nt) | hscC | Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| ? | NC_000913 | = 682798 | 107 (1.010) | coding (596/1671 nt) | hscC | Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor | |||||
| * | ? | NC_000913 | 1238953 = | 113 (1.000) | 3 (0.030) | 3/296 | 12.8 | 2.6% | coding (75/1071 nt) | dadX | alanine racemase, catabolic, PLP‑binding |
| ? | NC_000913 | 1238969 = | 114 (1.050) | coding (91/1071 nt) | dadX | alanine racemase, catabolic, PLP‑binding | |||||
| * | ? | NC_000913 | 1242815 = | 123 (1.090) | 3 (0.030) | 3/290 | 12.6 | 2.4% | coding (266/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | 1242848 = | 124 (1.160) | coding (233/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | 1247840 = | 88 (0.780) | 3 (0.030) | 3/292 | 12.7 | 3.6% | coding (1275/1419 nt) | dhaM | putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components |
| ? | NC_000913 | 1247877 = | 77 (0.720) | coding (1238/1419 nt) | dhaM | putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components | |||||
| * | ? | NC_000913 | 1512963 = | 123 (1.090) | 3 (0.030) | 3/286 | 12.5 | 2.7% | coding (147/1014 nt) | ydcT | putative ABC transporter ATPase |
| ? | NC_000913 | 1513028 = | 105 (1.000) | coding (212/1014 nt) | ydcT | putative ABC transporter ATPase | |||||
| * | ? | NC_000913 | = 1827132 | 96 (0.850) | 3 (0.030) | 3/288 | 12.6 | 3.3% | coding (1128/1344 nt) | astB | succinylarginine dihydrolase |
| ? | NC_000913 | = 1827166 | 87 (0.820) | coding (1094/1344 nt) | astB | succinylarginine dihydrolase | |||||
| * | ? | NC_000913 | = 1828681 | 115 (1.020) | 3 (0.030) | 3/288 | 12.6 | 2.7% | coding (1054/1479 nt) | astD | succinylglutamic semialdehyde dehydrogenase |
| ? | NC_000913 | = 1828695 | 109 (1.030) | coding (1040/1479 nt) | astD | succinylglutamic semialdehyde dehydrogenase | |||||
| * | ? | NC_000913 | 2268434 = | 133 (1.180) | 3 (0.030) | 3/290 | 12.6 | 2.3% | coding (606/987 nt) | yeiR | Zn‑stimulated GTPase involved in zinc homeostasis; mutants are cadmium and EDTA sensitive; Zn(2+) binding protein |
| ? | NC_000913 | 2268515 = | 133 (1.250) | coding (687/987 nt) | yeiR | Zn‑stimulated GTPase involved in zinc homeostasis; mutants are cadmium and EDTA sensitive; Zn(2+) binding protein | |||||
| * | ? | NC_000913 | 2303271 = | 86 (0.760) | 3 (0.030) | 3/298 | 12.8 | 3.4% | coding (227/495 nt) | napF | ferredoxin‑type protein, role in electron transfer to periplasmic nitrate reductase NapA |
| ? | NC_000913 | 2303335 = | 85 (0.780) | coding (163/495 nt) | napF | ferredoxin‑type protein, role in electron transfer to periplasmic nitrate reductase NapA | |||||
| * | ? | NC_000913 | = 2319247 | 114 (1.010) | 3 (0.030) | 3/290 | 12.6 | 2.6% | coding (630/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| ? | NC_000913 | = 2319264 | 117 (1.100) | coding (613/2850 nt) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN | |||||
| * | ? | NC_000913 | 2436503 = | 103 (0.920) | 3 (0.030) | 3/288 | 12.6 | 2.9% | coding (147/1014 nt) | usg | putative semialdehyde dehydrogenase |
| ? | NC_000913 | 2436529 = | 107 (1.010) | coding (121/1014 nt) | usg | putative semialdehyde dehydrogenase | |||||
| * | ? | NC_000913 | = 2796251 | 115 (1.020) | 3 (0.030) | 3/288 | 12.6 | 2.7% | coding (578/663 nt) | csiR | transcriptional repressor of csiD |
| ? | NC_000913 | = 2796261 | 109 (1.030) | coding (588/663 nt) | csiR | transcriptional repressor of csiD | |||||
| * | ? | NC_000913 | 2833080 = | 158 (1.400) | 3 (0.030) | 3/288 | 12.6 | 2.0% | coding (605/1440 nt) | norV | anaerobic nitric oxide reductase flavorubredoxin |
| ? | NC_000913 | 2833219 = | 151 (1.430) | coding (744/1440 nt) | norV | anaerobic nitric oxide reductase flavorubredoxin | |||||
| * | ? | NC_000913 | = 2919894 | 109 (0.970) | 3 (0.030) | 3/296 | 12.8 | 2.6% | coding (853/1341 nt) | gudX | glucarate dehydratase‑related protein, substrate unknown |
| ? | NC_000913 | = 2919904 | 115 (1.060) | coding (843/1341 nt) | gudX | glucarate dehydratase‑related protein, substrate unknown | |||||
| * | ? | NC_000913 | = 3008461 | 104 (0.920) | 3 (0.030) | 3/290 | 12.6 | 2.9% | coding (952/1197 nt) | ygeX | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| ? | NC_000913 | = 3008492 | 103 (0.970) | coding (983/1197 nt) | ygeX | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent | |||||
| * | ? | NC_000913 | 3368970 = | 96 (0.850) | 3 (0.030) | 3/282 | 12.4 | 3.5% | intergenic (+16/+44) | yhcG/yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily |
| ? | NC_000913 | 3368995 = | 77 (0.740) | intergenic (+41/+19) | yhcG/yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily | |||||
| * | ? | NC_000913 | = 3544651 | 119 (1.060) | 3 (0.030) | 3/288 | 12.6 | 2.6% | coding (194/771 nt) | bioH | pimeloyl‑ACP methyl ester carboxylesterase |
| ? | NC_000913 | = 3544692 | 112 (1.060) | coding (153/771 nt) | bioH | pimeloyl‑ACP methyl ester carboxylesterase | |||||
| * | ? | NC_000913 | 3558665 = | 122 (1.080) | 3 (0.030) | 3/298 | 12.8 | 2.3% | coding (398/1599 nt) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| ? | NC_000913 | 3558717 = | 132 (1.200) | coding (450/1599 nt) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression | |||||
| * | ? | NC_000913 | 3973849 = | 125 (1.110) | 3 (0.030) | 3/298 | 12.8 | 2.4% | coding (242/882 nt) | rffH | glucose‑1‑phosphate thymidylyltransferase |
| ? | NC_000913 | 3973867 = | 126 (1.150) | coding (260/882 nt) | rffH | glucose‑1‑phosphate thymidylyltransferase | |||||
| * | ? | NC_000913 | = 4054137 | 118 (1.050) | 3 (0.030) | 3/288 | 12.6 | 2.6% | coding (1142/1410 nt) | glnG | fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein |
| ? | NC_000913 | = 4054157 | 115 (1.090) | coding (1122/1410 nt) | glnG | fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein | |||||
| * | ? | NC_000913 | 4522458 = | 83 (0.740) | 3 (0.030) | 3/286 | 12.5 | 4.1% | coding (1637/1968 nt) | yjhG | putative dehydratase |
| ? | NC_000913 | 4522501 = | 63 (0.600) | coding (1594/1968 nt) | yjhG | putative dehydratase | |||||