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 | 16.0% | 24.1 ‑14.0 0.0 | 164 | A28A (GCT→GCC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,522 | 0 | C→G | 11.6% | 14.9 ‑9.6 0.0 | 164 | L29V (CTG→GTG) | yidX | putative lipoprotein |
| * | NC_000913 | 3,608,682 | 0 | T→C | 14.4% | 14.3 ‑12.4 0.0 | 98 | intergenic (+33/+69) | zntA/tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| * | NC_000913 | 3,781,152 | 0 | A→G | 14.9% | 10.4 ‑28.0 ‑0.0 | 97 | intergenic (+135/‑63) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 720,974 | 0 | T→G | 100.0% | 2.5 | 1 | intergenic (+134/+82) | ybfK/kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| * | NC_000913 | 720,971 | 0 | A→G | 100.0% | 1.7 | 1 | intergenic (+131/+85) | ybfK/kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| * | NC_000913 | 720,969 | 0 | T→G | 100.0% | 1.5 | 1 | intergenic (+129/+87) | ybfK/kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| * | NC_000913 | 1,433,921 | 0 | G→T | 100.0% | 1.3 | 1 | intergenic (‑247/+70) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage |
| * | NC_000913 | 720,961 | 0 | T→A | 100.0% | 0.6 | 1 | intergenic (+121/+95) | ybfK/kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| * | NC_000913 | 720,958 | 0 | A→G | 100.0% | 0.5 | 1 | intergenic (+118/+98) | ybfK/kdpE | uncharacterized protein/response regulator in two‑component regulatory system with KdpD |
| * | NC_000913 | 4,171,387 | 0 | G→A | 100.0% | ‑0.5 | 1 | noncoding (2747/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,391 | 0 | G→A | 100.0% | ‑0.5 | 1 | noncoding (2751/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,392 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2752/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,394 | 0 | T→A | 100.0% | ‑0.5 | 1 | noncoding (2754/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,395 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2755/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,396 | 0 | T→A | 100.0% | ‑0.5 | 1 | noncoding (2756/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,399 | 0 | G→A | 100.0% | ‑0.5 | 1 | noncoding (2759/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,400 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2760/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,402 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2762/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,403 | 0 | G→A | 100.0% | ‑0.5 | 1 | noncoding (2763/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,407 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2767/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,408 | 0 | T→A | 100.0% | ‑0.5 | 1 | noncoding (2768/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,409 | 0 | T→A | 100.0% | ‑0.5 | 1 | noncoding (2769/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,410 | 0 | G→A | 100.0% | ‑0.5 | 1 | noncoding (2770/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| * | NC_000913 | 4,171,411 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2771/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C→T | 16.2% | 68.1 0.0 ‑0.3 | 160 | 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) | 36 (0.300) | 27/282 | 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 | = 1299498 | 0 (0.000) | 22 (0.180) | 20/290 | 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 | 4409174 = | NA (NA) | 12 (0.110) | 8/268 | 9.2 | 8.3% | 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 = | 133 (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 | = 381689 | NA (NA) | 11 (0.090) | 8/280 | 9.5 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1430276 = | 89 (0.710) | 6 (0.050) | 5/280 | 11.1 | 6.1% | coding (1228/3363 nt) | stfR | Rac prophage; putative tail fiber protein |
| ? | NC_000913 | 1430422 = | 101 (0.860) | coding (1374/3363 nt) | stfR | Rac prophage; putative tail fiber protein | |||||
| * | ? | NC_000913 | = 3686344 | 103 (0.820) | 6 (0.050) | 5/278 | 11.1 | 5.9% | coding (2830/3474 nt) | bcsC | cellulose synthase subunit |
| ? | NC_000913 | = 3686424 | 97 (0.830) | coding (2750/3474 nt) | bcsC | cellulose synthase subunit | |||||
| * | ? | NC_000913 | = 2331858 | 107 (0.860) | 5 (0.040) | 5/282 | 11.2 | 4.6% | pseudogene (2545/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| ? | NC_000913 | = 2331859 | 106 (0.900) | pseudogene (2544/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein | |||||
| * | ? | NC_000913 | 2897255 = | 110 (0.880) | 5 (0.040) | 5/282 | 11.2 | 4.5% | coding (616/1338 nt) | ygcS | putative MFS sugar transporter; membrane protein |
| ? | NC_000913 | 2897354 = | 108 (0.910) | coding (517/1338 nt) | ygcS | putative MFS sugar transporter; membrane protein | |||||
| * | ? | NC_000913 | 3927418 = | 109 (0.870) | 5 (0.040) | 5/274 | 11.0 | 4.4% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 118 (1.030) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | = 1402855 | 103 (0.820) | 5 (0.040) | 4/282 | 11.9 | 4.8% | coding (401/1446 nt) | abgB | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| ? | NC_000913 | = 1402899 | 103 (0.870) | coding (357/1446 nt) | abgB | p‑aminobenzoyl‑glutamate hydrolase, B subunit | |||||
| * | ? | NC_000913 | = 1946034 | 92 (0.740) | 5 (0.040) | 4/282 | 11.9 | 5.7% | intergenic (‑58/+81) | ruvA/yobI | component of RuvABC resolvasome, regulatory subunit/uncharacterized protein |
| ? | NC_000913 | = 1946036 | 77 (0.650) | intergenic (‑60/+79) | ruvA/yobI | component of RuvABC resolvasome, regulatory subunit/uncharacterized protein | |||||
| * | ? | NC_000913 | = 307363 | 101 (0.810) | 4 (0.030) | 4/282 | 11.9 | 4.0% | coding (1970/2526 nt) | ecpC | ECP production outer membrane protein |
| ? | NC_000913 | = 307376 | 94 (0.790) | coding (1957/2526 nt) | ecpC | ECP production outer membrane protein | |||||
| * | ? | NC_000913 | 603377 = | 153 (1.220) | 4 (0.040) | 4/270 | 11.5 | 2.8% | intergenic (+42/+39) | pheP/ybdG | phenylalanine transporter/mechanosensitive channel protein, miniconductance |
| ? | NC_000913 | 603410 = | 144 (1.270) | intergenic (+75/+6) | pheP/ybdG | phenylalanine transporter/mechanosensitive channel protein, miniconductance | |||||
| * | ? | NC_000913 | = 2962469 | 107 (0.860) | 4 (0.030) | 4/280 | 11.8 | 3.6% | coding (296/324 nt) | ppdC | putative prepilin peptidase‑dependent protein |
| ? | NC_000913 | = 2962525 | 113 (0.960) | coding (240/324 nt) | ppdC | putative prepilin peptidase‑dependent protein | |||||
| * | ? | NC_000913 | = 3529405 | 100 (0.800) | 4 (0.030) | 4/278 | 11.8 | 4.2% | coding (58/402 nt) | hslR | ribosome‑associated heat shock protein Hsp15 |
| ? | NC_000913 | = 3529461 | 87 (0.750) | coding (114/402 nt) | hslR | ribosome‑associated heat shock protein Hsp15 | |||||
| * | ? | NC_000913 | 84602 = | 141 (1.130) | 3 (0.030) | 3/278 | 12.5 | 2.0% | coding (235/945 nt) | leuO | global transcription factor |
| ? | NC_000913 | 84698 = | 165 (1.410) | coding (331/945 nt) | leuO | global transcription factor | |||||
| * | ? | NC_000913 | 909017 = | 77 (0.620) | 3 (0.030) | 3/284 | 12.7 | 3.9% | coding (278/1002 nt) | ltaE | L‑allo‑threonine aldolase, PLP‑dependent |
| ? | NC_000913 | 909055 = | 76 (0.640) | coding (240/1002 nt) | ltaE | L‑allo‑threonine aldolase, PLP‑dependent | |||||
| * | ? | NC_000913 | = 957583 | 153 (1.220) | 3 (0.030) | 3/284 | 12.7 | 2.1% | intergenic (+129/‑70) | ycaP/serC | UPF0702 family putative inner membrane protein/3‑phosphoserine/phosphohydroxythreonine aminotransferase |
| ? | NC_000913 | = 957595 | 135 (1.130) | intergenic (+141/‑58) | ycaP/serC | UPF0702 family putative inner membrane protein/3‑phosphoserine/phosphohydroxythreonine aminotransferase | |||||
| * | ? | NC_000913 | = 1789015 | 110 (0.880) | 3 (0.030) | 3/284 | 12.7 | 2.8% | coding (581/1047 nt) | aroH | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible |
| ? | NC_000913 | = 1789028 | 101 (0.850) | coding (594/1047 nt) | aroH | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible | |||||
| * | ? | NC_000913 | 2180180 = | 121 (0.970) | 3 (0.030) | 3/280 | 12.5 | 2.5% | coding (86/1005 nt) | yegU | ADP‑ribosylglycohydrolase family protein |
| ? | NC_000913 | 2180247 = | 122 (1.040) | coding (153/1005 nt) | yegU | ADP‑ribosylglycohydrolase family protein | |||||
| * | ? | NC_000913 | 2704871 = | 143 (1.140) | 3 (0.030) | 3/284 | 12.7 | 2.1% | coding (439/975 nt) | lepB | leader peptidase (signal peptidase I) |
| ? | NC_000913 | 2704888 = | 150 (1.260) | coding (422/975 nt) | lepB | leader peptidase (signal peptidase I) | |||||
| * | ? | NC_000913 | 2765420 = | 140 (1.120) | 3 (0.030) | 3/210 | 10.4 | 3.2% | intergenic (‑267/+93) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| ? | NC_000913 | = 2765411 | 82 (0.930) | intergenic (‑258/+102) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | = 2800514 | 108 (0.860) | 3 (0.030) | 3/280 | 12.5 | 2.8% | intergenic (+39/‑209) | ygaM/nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein |
| ? | NC_000913 | = 2800519 | 105 (0.890) | intergenic (+44/‑204) | ygaM/nrdH | putative membrane‑anchored DUF883 family ribosome‑binding protein/hydrogen donor for NrdEF electron transport system; glutaredoxin‑like protein | |||||
| * | ? | NC_000913 | = 2911751 | 98 (0.780) | 3 (0.030) | 3/282 | 12.6 | 3.3% | coding (1901/2235 nt) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| ? | NC_000913 | = 2911761 | 83 (0.700) | coding (1891/2235 nt) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase | |||||
| * | ? | NC_000913 | 2945975 = | 115 (0.920) | 3 (0.020) | 3/288 | 12.8 | 2.6% | noncoding (80/97 nt) | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 2945999 = | 112 (0.930) | intergenic (‑157/+82) | tcdA/mltA | tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A | |||||
| * | ? | NC_000913 | = 3044727 | 115 (0.920) | 3 (0.020) | 3/294 | 12.9 | 2.6% | coding (1066/1440 nt) | bglA | 6‑phospho‑beta‑glucosidase A |
| ? | NC_000913 | 3044731 = | 112 (0.910) | coding (1070/1440 nt) | bglA | 6‑phospho‑beta‑glucosidase A | |||||
| * | ? | NC_000913 | 3344992 = | 127 (1.020) | 3 (0.030) | 3/278 | 12.5 | 2.6% | coding (276/1434 nt) | rpoN | RNA polymerase, sigma 54 (sigma N) factor |
| ? | NC_000913 | 3345024 = | 110 (0.940) | coding (308/1434 nt) | rpoN | RNA polymerase, sigma 54 (sigma N) factor | |||||
| * | ? | NC_000913 | 3368970 = | 142 (1.140) | 3 (0.030) | 3/274 | 12.4 | 2.1% | intergenic (+16/+44) | yhcG/yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily |
| ? | NC_000913 | 3368995 = | 144 (1.250) | intergenic (+41/+19) | yhcG/yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily | |||||
| * | ? | NC_000913 | 3484544 = | 139 (1.110) | 3 (0.030) | 3/278 | 12.5 | 2.3% | coding (55/870 nt) | prkB | putative phosphoribulokinase |
| ? | NC_000913 | = 3484540 | 126 (1.080) | coding (51/870 nt) | prkB | putative phosphoribulokinase | |||||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 4 (0.030) | 3/280 | 12.5 | 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 | = 4192747 | 103 (0.820) | 3 (0.030) | 3/282 | 12.6 | 3.0% | coding (91/201 nt) | thiS | immediate sulfur donor in thiazole formation |
| ? | NC_000913 | = 4192865 | 98 (0.830) | coding (712/756 nt) | thiF | adenylyltransferase, modifies ThiS C‑terminus | |||||
| * | ? | NC_000913 | 4345944 = | 117 (0.940) | 3 (0.030) | 3/266 | 12.2 | 2.9% | coding (1383/1647 nt) | fumB | anaerobic class I fumarate hydratase (fumarase B) |
| ? | NC_000913 | 4345960 = | 96 (0.860) | coding (1367/1647 nt) | fumB | anaerobic class I fumarate hydratase (fumarase B) | |||||
| * | ? | NC_000913 | 4362751 = | 98 (0.780) | 3 (0.030) | 3/284 | 12.7 | 3.1% | coding (558/576 nt) | yjdC | putative transcriptional regulator |
| ? | NC_000913 | 4362790 = | 97 (0.810) | coding (519/576 nt) | yjdC | putative transcriptional regulator | |||||
| * | ? | NC_000913 | = 4481898 | 135 (1.080) | 3 (0.030) | 3/282 | 12.6 | 2.5% | coding (1940/2856 nt) | valS | valyl‑tRNA synthetase |
| ? | NC_000913 | = 4481970 | 109 (0.920) | coding (1868/2856 nt) | valS | valyl‑tRNA synthetase | |||||
| * | ? | NC_000913 | 4542682 = | 16 (0.130) | 3 (0.030) | 3/280 | 12.5 | 4.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 108 (0.920) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||