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 46 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 51.9% | 14.3 / 103.2 | 77 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 48.4% | 21.4 / 122.9 | 91 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 699,722 | 0 | A | G | 40.4% | 26.7 / 58.5 | 57 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 40.2% | 76.2 / 104.7 | 97 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 5,740,467 | 0 | T | G | 38.7% | 9.6 / 26.2 | 31 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 195,559 | 0 | C | A | 36.5% | 79.4 / 66.2 | 63 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,485,154 | 0 | T | C | 32.4% | 35.4 / 24.0 | 36 | intergenic (+60/‑87) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 5,485,159 | 0 | G | A | 32.3% | 32.3 / 19.7 | 36 | intergenic (+65/‑82) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 5,485,167 | 0 | G | A | 32.1% | 30.6 / 18.0 | 32 | intergenic (+73/‑74) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 5,485,150 | 0 | A | G | 31.7% | 46.1 / 27.2 | 41 | intergenic (+56/‑91) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 5,485,162 | 0 | T | C | 30.6% | 40.5 / 23.2 | 36 | intergenic (+68/‑79) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 5,485,153 | 0 | A | G | 28.9% | 45.8 / 23.7 | 40 | intergenic (+59/‑88) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 4,340,081 | 0 | A | G | 28.6% | 32.7 / 15.5 | 30 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 5,740,471 | 0 | A | T | 28.6% | 32.0 / 11.7 | 32 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 5,485,168 | 0 | C | T | 28.1% | 41.9 / 18.3 | 32 | intergenic (+74/‑73) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 5,485,171 | 0 | C | T | 28.1% | 35.7 / 17.6 | 32 | intergenic (+77/‑70) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 4,583,571 | 0 | G | . | 27.8% | 37.0 / 13.3 | 18 | intergenic (‑144/+27) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| * | NC_002947 | 4,340,089 | 0 | G | C | 26.5% | 47.7 / 16.6 | 35 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,821,395 | 0 | G | . | 26.3% | 40.1 / 13.8 | 19 | intergenic (‑64/‑327) | PP_2474/PP_2475 | glutathione S‑transferase family protein/TetR family transcriptional regulator |
| * | NC_002947 | 5,740,470 | 0 | A | T | 25.8% | 43.7 / 12.0 | 32 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 509 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4586029 | 8 (0.130) | 29 (0.500) | 18/256 | 3.3 | 62.8% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 27 (0.470) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 1499436 = | 43 (0.680) | 29 (0.500) | 17/258 | 3.6 | 50.9% | intergenic (+13/‑151) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | 1499517 = | 16 (0.270) | intergenic (+94/‑70) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | 1499507 = | 19 (0.300) | 29 (0.500) | 15/254 | 4.0 | 37.3% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 6060505 | 80 (1.390) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | 4896378 = | 44 (0.700) | 14 (0.260) | 13/236 | 4.2 | 32.0% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | 4896467 = | 22 (0.410) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 2048810 | 65 (1.030) | 12 (0.220) | 11/244 | 5.0 | 19.2% | intergenic (+49/+90) | PP_1821/PP_1822 | glutathione S‑transferase family protein/hypothetical protein |
| ? | NC_002947 | = 2048867 | 44 (0.800) | intergenic (+106/+33) | PP_1821/PP_1822 | glutathione S‑transferase family protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 1499458 | 31 (0.490) | 14 (0.230) | 13/274 | 5.0 | 37.6% | intergenic (+35/‑129) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 1499495 | 16 (0.260) | intergenic (+72/‑92) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
| * | ? | NC_002947 | 1499507 = | 19 (0.300) | 28 (0.490) | 11/254 | 5.2 | 44.3% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | 5786483 = | 53 (0.920) | intergenic (+26/‑105) | PP_5068/trxC | hypothetical protein/thioredoxin | |||||
| * | ? | NC_002947 | 1499507 = | 19 (0.300) | 29 (0.500) | 11/254 | 5.2 | 62.1% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | 2301507 = | 18 (0.310) | intergenic (‑151/‑180) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein | |||||
| * | ? | NC_002947 | 1499507 = | 19 (0.300) | 28 (0.490) | 11/254 | 5.2 | 55.8% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | 2236933 = | 27 (0.470) | intergenic (+28/+100) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter | |||||
| * | ? | NC_002947 | = 1436099 | 79 (1.250) | 29 (0.500) | 11/254 | 5.2 | 39.7% | intergenic (‑136/+17) | PP_1256/PP_1257 | alpha‑ketoglutarate semialdehyde dehydrogenase/1‑pyrroline‑4‑hydroxy‑2‑carboxylate deaminase |
| ? | NC_002947 | 1499519 = | 16 (0.280) | intergenic (+96/‑68) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||