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 157 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,725 | 0 | A | G | 51.3% | 7.3 / inf | 372 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 49.8% | 202.3 / inf | 473 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,808,226 | 0 | A | G | 49.2% | ‑1.5 / 94.4 | 68 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,348,749 | 0 | A | G | 49.1% | 214.4 / inf | 531 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,808,225 | 0 | A | C | 48.5% | 3.7 / 99.6 | 68 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 2,282,813 | 0 | T | G | 45.0% | 64.4 / 270.1 | 192 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,340,127 | 0 | A | G | 44.1% | 72.9 / 147.7 | 121 | 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 | 43.7% | 74.5 / 151.5 | 121 | 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 | 43.6% | 72.5 / 146.3 | 121 | 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 | 43.5% | 90.9 / 173.9 | 125 | 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 | 43.1% | 85.5 / 147.9 | 125 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,340,119 | 0 | A | T | 43.0% | 94.4 / 165.6 | 133 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 3,817,681 | 0 | C | G | 42.4% | 25.6 / 42.1 | 33 | F207L (TTC→TTG) | bamA‑II | outer membrane protein assembly factor |
| * | NC_002947 | 1,544,543 | 0 | G | C | 42.3% | 124.4 / 237.6 | 183 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,340,133 | 0 | G | C | 41.8% | 114.2 / 178.0 | 135 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 195,634 | 0 | C | T | 41.7% | 363.1 / inf | 532 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,740,527 | 0 | A | T | 41.7% | 66.8 / 150.2 | 157 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 2,282,818 | 0 | G | C | 41.1% | 127.9 / 218.0 | 165 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,282,817 | 0 | G | C | 40.8% | 128.5 / 216.4 | 165 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,544,536 | 0 | C | G | 40.7% | 161.8 / 239.8 | 183 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| Marginal new junction evidence (lowest skew 10 of 580 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808219 = | 51 (0.160) | 114 (0.480) | 51/224 | 6.2 | 52.7% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 166 (0.690) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4896423 = | 168 (0.530) | 59 (0.220) | 31/252 | 12.8 | 29.3% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896512 = | 140 (0.520) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 4808224 | 56 (0.180) | 107 (0.370) +CGGCGCTTCGCGG |
31/268 | 13.7 | 51.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4945261 = | 162 (0.510) | intergenic (+576/+222) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947 | 1114875 = | 169 (0.540) | 49 (0.190) | 23/244 | 15.3 | 26.4% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | 1114951 = | 133 (0.510) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
| * | ? | NC_002947 | = 4896443 | 163 (0.520) | 54 (0.200) | 23/252 | 15.7 | 27.2% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 149 (0.550) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 4647603 = | 111 (0.350) | 57 (0.250) | 18/216 | 15.7 | 35.2% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647711 = | 128 (0.550) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | 5162618 = | 126 (0.400) | 44 (0.170) | 21/242 | 16.0 | 27.1% | intergenic (+93/+108) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| ? | NC_002947 | 5162702 = | 133 (0.510) | intergenic (+177/+24) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase | |||||
| * | ? | NC_002947 | = 5914240 | 178 (0.570) | 26 (0.100) | 20/238 | 16.1 | 15.3% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | = 5914280 | 144 (0.570) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | = 295713 | 311 (0.990) | 43 (0.150) | 24/266 | 16.1 | 12.9% | intergenic (+60/+82) | PP_0241/PP_0242 | transporter/TetR family transcriptional regulator |
| ? | NC_002947 | = 295744 | 297 (1.040) | intergenic (+91/+51) | PP_0241/PP_0242 | transporter/TetR family transcriptional regulator | |||||
| * | ? | NC_002947 | 4586063 = | 156 (0.500) | 30 (0.130) | 17/218 | 16.3 | 26.0% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586167 = | 55 (0.240) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||