mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 210 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,348,749 | 0 | A | G | 50.9% | 145.8 / inf | 517 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 49.7% | 197.9 / inf | 449 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,340,127 | 0 | A | G | 49.3% | 50.0 / 202.5 | 142 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,128 | 0 | C | T | 48.9% | 45.2 / 203.4 | 142 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,126 | 0 | C | T | 48.6% | 52.0 / 204.8 | 144 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,120 | 0 | G | C | 47.9% | 85.1 / 231.8 | 146 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,125 | 0 | A | G | 47.9% | 63.9 / 202.2 | 146 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,808,226 | 0 | A | G | 47.9% | 5.1 / 96.3 | 71 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 699,725 | 0 | A | G | 47.4% | 111.6 / inf | 388 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,808,225 | 0 | A | C | 46.5% | 9.1 / 104.9 | 71 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,340,119 | 0 | A | T | 46.4% | 98.1 / 206.9 | 151 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,013,252 | 0 | T | G | 46.0% | 99.5 / 239.0 | 164 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 2,282,813 | 0 | T | G | 45.8% | 104.3 / 295.1 | 213 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,340,134 | 0 | A | T | 44.9% | 115.1 / 206.6 | 156 | intergenic (+75/‑256) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,133 | 0 | G | C | 44.6% | 126.6 / 228.2 | 157 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,403,596 | 0 | G | A | 43.4% | 99.7 / 268.6 | 221 | intergenic (‑56/+25) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 1,403,597 | 0 | T | C | 43.1% | 89.3 / 265.5 | 223 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 1,544,546 | 0 | T | G | 42.8% | 140.9 / 306.6 | 222 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,013,251 | 0 | A | T | 41.9% | 149.5 / 224.7 | 185 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 5,740,527 | 0 | A | T | 41.1% | 61.4 / 157.9 | 146 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 653 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 49 (0.170) | 117 (0.530) | 48/220 | 6.0 | 51.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 183 (0.830) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808224 | 37 (0.130) | 155 (0.580) | 53/266 | 7.3 | 54.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 228 (0.850) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 228 (0.780) | 111 (0.440) | 48/250 | 7.5 | 52.9% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808204 | 1 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808224 | 37 (0.130) | 143 (0.570) | 34/250 | 11.0 | 52.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5989005 | 224 (0.890) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5513315 | 206 (0.700) | 39 (0.160) | 27/238 | 12.6 | 18.8% | intergenic (+45/‑109) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein |
| ? | NC_002947 | = 5513371 | 168 (0.700) | intergenic (+101/‑53) | urtD/urtE | ABC transporter ATP‑binding protein/ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947 | 181660 = | NA (NA) | 23 (0.130) +54 bp |
17/182 | 13.0 | 14.1% | intergenic (+126/‑7) | PP_23SB/PP_r01 | 23S ribosomal RNA/5S ribosomal RNA |
| ? | NC_002947 | 181793 = | 225 (0.770) | intergenic (+7/‑99) | PP_r01/PP_5SB | 5S ribosomal RNA/5S ribosomal RNA | |||||
| * | ? | NC_002947 | 4586063 = | 166 (0.570) | 45 (0.210) | 21/214 | 13.4 | 32.5% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 65 (0.300) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 295713 | 238 (0.810) | 40 (0.150) | 28/262 | 13.5 | 15.1% | intergenic (+60/+82) | PP_0241/PP_0242 | transporter/TetR family transcriptional regulator |
| ? | NC_002947 | = 295744 | 236 (0.890) | intergenic (+91/+51) | PP_0241/PP_0242 | transporter/TetR family transcriptional regulator | |||||
| * | ? | NC_002947 | 4896423 = | 148 (0.510) | 44 (0.180) | 25/248 | 13.8 | 25.3% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 134 (0.540) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 3947957 = | 144 (0.490) | 36 (0.150) | 22/234 | 14.2 | 24.0% | coding (136/1797 nt) | PP_3483 | type II secretion system protein |
| ? | NC_002947 | 3948042 = | 112 (0.480) | coding (51/1797 nt) | PP_3483 | type II secretion system protein | |||||