mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 195,634 | 0 | C | T | 49.3% | 19.8 / 102.1 | 75 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,327,121 | 0 | C | T | 48.9% | 33.9 / 126.7 | 94 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 46.9% | 9.6 / 81.3 | 64 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 44.0% | 52.7 / 108.2 | 91 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,544,501 | 0 | G | C | 40.0% | 15.7 / 24.0 | 25 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,489 | 0 | C | A | 37.5% | 14.1 / 22.3 | 24 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 195,559 | 0 | C | A | 36.5% | 83.6 / 59.0 | 63 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,492 | 0 | G | C | 36.0% | 19.6 / 22.6 | 25 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,494 | 0 | C | G | 36.0% | 20.3 / 19.8 | 25 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,499 | 0 | C | G | 36.0% | 14.6 / 22.1 | 25 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,504 | 0 | T | G | 35.5% | 23.9 / 27.2 | 31 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 181,805 | 0 | T | C | 29.3% | 54.2 / 26.9 | 42 | intergenic (+19/‑87) | PP_r01/PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| * | NC_002947 | 181,812 | 0 | A | G | 28.2% | 51.5 / 23.2 | 40 | intergenic (+26/‑80) | PP_r01/PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| * | NC_002947 | 181,818 | 0 | G | A | 28.2% | 54.9 / 21.6 | 39 | intergenic (+32/‑74) | PP_r01/PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| * | NC_002947 | 4,340,089 | 0 | G | C | 28.1% | 43.2 / 11.5 | 32 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,081 | 0 | A | G | 28.0% | 31.9 / 10.1 | 28 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 5,988,895 | 0 | A | G | 27.8% | 74.0 / 35.3 | 55 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 181,811 | 0 | C | T | 27.5% | 55.6 / 21.6 | 40 | intergenic (+25/‑81) | PP_r01/PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| * | NC_002947 | 5,903,165 | 0 | A | C | 26.9% | 66.9 / 26.0 | 52 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 26.7% | 90.5 / 36.6 | 60 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 277 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4893553 = | 51 (0.960) | 8 (0.190) | 7/230 | 4.8 | 18.1% | intergenic (+28/‑180) | pyk/PP_4302 | pyruvate kinase/urea transporter |
| ? | NC_002947 | 4893632 = | 31 (0.720) | intergenic (+107/‑101) | pyk/PP_4302 | pyruvate kinase/urea transporter | |||||
| * | ? | NC_002947 | = 652782 | 38 (0.720) | 9 (0.200) | 7/244 | 5.1 | 35.5% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 5594092 = | 38 (0.720) | 10 (0.230) | 6/228 | 5.2 | 24.5% | intergenic (‑39/+106) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947 | 5594185 = | 31 (0.730) | intergenic (‑132/+13) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947 | 3947913 = | 27 (0.510) | 7 (0.160) | 6/228 | 5.2 | 25.6% | coding (136/1797 nt) | PP_3483 | type II secretion system protein |
| ? | NC_002947 | 3947998 = | 19 (0.450) | coding (51/1797 nt) | PP_3483 | type II secretion system protein | |||||
| * | ? | NC_002947 | = 2236934 | 49 (0.920) | 10 (0.210) | 7/252 | 5.3 | 18.4% | intergenic (+29/+99) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter |
| ? | NC_002947 | = 2236993 | 45 (0.960) | intergenic (+88/+40) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter | |||||
| * | ? | NC_002947 | 6058676 = | 40 (0.750) | 9 (0.190) | 7/258 | 5.4 | 18.9% | coding (1873/2079 nt) | recG | junction‑specific ATP‑dependent DNA helicase |
| ? | NC_002947 | 6058745 = | 41 (0.850) | coding (1942/2079 nt) | recG | junction‑specific ATP‑dependent DNA helicase | |||||
| * | ? | NC_002947 | = 4094636 | 67 (1.260) | 8 (0.150) | 8/280 | 5.4 | 11.8% | intergenic (+52/+83) | PP_3602/PP_3603 | 2,5‑dioxovalerate dehydrogenase/GntR family transcriptional regulator |
| ? | NC_002947 | = 4094707 | 53 (1.010) | intergenic (+123/+12) | PP_3602/PP_3603 | 2,5‑dioxovalerate dehydrogenase/GntR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 14 (0.290) | 7/260 | 5.5 | 35.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 50 (1.030) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 1499507 = | 23 (0.430) | 8 (0.160) | 7/260 | 5.5 | 18.6% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 6060505 | 49 (1.010) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | 4936617 = | 45 (0.850) | 7 (0.140) | 7/266 | 5.6 | 14.3% | intergenic (‑28/‑390) | flhA/PP_4345 | flagellar export pore protein/GntR family transcriptional regulator |
| ? | NC_002947 | 4936640 = | 42 (0.850) | intergenic (‑51/‑367) | flhA/PP_4345 | flagellar export pore protein/GntR family transcriptional regulator | |||||