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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 19,009 | C→T | 100% | S222F (TCC→TTC) | yybT → | DHH subfamily phosphodiesterase |
| RA | 39,653 | C→A | 100% | S494I (AGT→ATT) | mecA ← | penicillin binding protein 2 prime |
| RA | 110,660 | T→A | 13.0% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,904 | G→T | 51.7% | D255Y (GAT→TAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 37.0% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 33.9% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 119,853 | C→A | 38.7% | G254W (GGG→TGG) | yjbB ← | possible PnaS family phosphate:sodium (Na+) symporter |
| RA | 328,487 | C→A | 19.4% | I210I (ATC→ATA) | USA300HOU_0294 → | hypothetical membrane protein |
| RA | 478,502 | C→A | 90.4% | D342E (GAC→GAA) | ndhF → | NADH dehydrogenase (ubiquinone) |
| RA | 509,502 | T→C | 10.5% | I85T (ATT→ACT) | dnaZX → | DNA‑directed DNA polymerase III gamma and tau subunits |
| RA | 512,643 | A→G | 54.8% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 707,909 | A→T | 100% | M1M (TTG→ATG) † | mntB ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 762,336 | A→G | 7.1% | H162R (CAT→CGT) | ycsN → | possible aldo/keto reductase |
| RA | 770,855 | A→G | 9.6% | intergenic (+41/‑212) | ebsC → / → fruR | possible transcriptional regulator/DeoR family transcriptional regulator |
| RA | 770,860 | G→A | 9.5% | intergenic (+46/‑207) | ebsC → / → fruR | possible transcriptional regulator/DeoR family transcriptional regulator |
| RA | 849,656 | G→A | 56.8% | G261D (GGT→GAT) | yvcJ → | ATP‑binding protein |
| RA | 865,305 | T→G | 10.5% | S207S (TCT→TCG) | est → | carboxylesterase |
| RA | 937,158 | T→A | 7.5% | intergenic (+65/‑1952) | yumB → / → USA300HOU_0903 | NADH dehydrogenase/NhaC family sodium:proton (Na+:H+) antiporter |
| RA | 950,093 | T→A | 8.8% | intergenic (+880/‑275) | prsA1 → / → yqiG | peptidylprolyl isomerase/flavin reductase |
| RA | 950,098 | T→A | 9.3% | intergenic (+885/‑270) | prsA1 → / → yqiG | peptidylprolyl isomerase/flavin reductase |
| RA | 973,213 | C→A | 100% | E175* (GAG→TAG) | yitU ← | possible HAD superfamily hydrolase |
| RA | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,047,955 | G→A | 8.2% | D324N (GAT→AAT) | menF → | isochorismate synthase |
| RA | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,196,508 | C→A | 100% | intergenic (+2563/‑1229) | ftsQ → / → ylmE | cell division protein FtsQ/hypothetical protein |
| RA | 1,200,415 | C→T | 18.0% | A77V (GCT→GTT) | ylmH → | hypothetical protein |
| RA | 1,231,411 | A→G | 100% | D19G (GAT→GGT) | prpC → | possible PP2C protein phosphatase |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,478,171 | T→G | 9.1% | A7951A (GCA→GCC) | ebh ← | extracellular matrix binding protein |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_1405 | chorismate synthase/hypothetical protein |
| RA | 1,643,049 | G→A | 25.4% | A341V (GCT→GTT) | accC ← | biotin carboxylase |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| JC | 1,747,374 | Δ3 bp | 44.3% | coding (2073‑2075/2280 nt) | secDF ← | RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter |
| RA | 1,794,352 | A→T | 9.6% | Y431N (TAT→AAT) | USA300HOU_1678 ← | hypothetical membrane protein |
| RA | 1,828,478 | T→C | 11.8% | I192M (ATA→ATG) | csd2 ← | cysteine desulfurase |
| RA | 1,909,214 | C→A | 54.7% | Y7* (TAC→TAA) | USA300HOU_1771 → | hypothetical membrane protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,027,805 | C→A | 100% | V48F (GTT→TTT) | vraS ← | sensor histidine kinase VraS |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,337,959 | C→T | 100% | intergenic (‑125/‑119) | adhR ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,343,438 | C→T | 100% | intergenic (+114/+250) | USA300HOU_2200 → / ← alsD | hypothetical protein/acetolactate decarboxylase |
| RA | 2,361,590 | C→T | 55.0% | R239H (CGT→CAT) | secY1 ← | Sec family Type I general secretory pathway preprotein translocase SecY |
| RA | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,756,983 | A→G | 9.9% | intergenic (‑85/+15) | USA300HOU_2612 ← / ← nrdG | hypothetical protein/anaerobic ribonucleotide reductase small subunit |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 14186 | 45 (1.080) | 4 (0.100) | 4/240 | NT | 8.5% | intergenic (+87/‑563) | serS/azlC | serine‑‑tRNA ligase/LIV‑E family branched chain amino acid exporter |
| ? | CP000730 | = 14200 | 44 (1.140) | intergenic (+101/‑549) | serS/azlC | serine‑‑tRNA ligase/LIV‑E family branched chain amino acid exporter | |||||
| * | ? | CP000730 | 441295 = | 37 (0.890) | 3 (0.080) | 5/240 | NT | 8.9% | intergenic (+12/+101) | guaA/USA300HOU_0415 | GMP synthase (glutamine‑hydrolyzing)/hypothetical protein |
| ? | CP000730 | 441323 = | 27 (0.700) | intergenic (+40/+73) | guaA/USA300HOU_0415 | GMP synthase (glutamine‑hydrolyzing)/hypothetical protein | |||||
| * | ? | CP000730 | 512620 = | 49 (1.180) | 38 (1.330) +40 bp |
30/178 | NT | 53.0% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 1998278 = | NA (NA) | intergenic (‑6/+5) | USA300HOU_t0050/rrf4 | tRNA‑Val/5S ribosomal RNA | |||||
| * | ? | CP000730 | 528464 = | 34 (0.820) | 3 (0.080) | 3/230 | NT | 9.8% | intergenic (+5/‑162) | tatD/rnmV | TatD family deoxyribonuclease/hypothetical protein |
| ? | CP000730 | 528541 = | 25 (0.670) | intergenic (+82/‑85) | tatD/rnmV | TatD family deoxyribonuclease/hypothetical protein | |||||
| * | ? | CP000730 | 553211 = | 53 (1.270) | 3 (0.080) | 3/236 | NT | 6.2% | intergenic (+178/‑2881) | folB/rrf2 | dihydroneopterin aldolase/5S ribosomal RNA |
| ? | CP000730 | 553257 = | 43 (1.130) | intergenic (+224/‑2835) | folB/rrf2 | dihydroneopterin aldolase/5S ribosomal RNA | |||||
| * | ? | CP000730 | 904166 = | 39 (0.940) | 3 (0.080) | 3/230 | NT | 7.8% | intergenic (+441/‑230) | USA300HOU_0861/USA300HOU_0862 | possible DNA primase/hypothetical protein |
| ? | CP000730 | 904273 = | 36 (0.970) | intergenic (+548/‑123) | USA300HOU_0861/USA300HOU_0862 | possible DNA primase/hypothetical protein | |||||
| * | ? | CP000730 | 1009804 = | 45 (1.080) | 3 (0.080) | 3/238 | NT | 6.9% | coding (82/855 nt) | rluA1 | pseudouridylate synthase |
| ? | CP000730 | 1009828 = | 40 (1.040) | coding (106/855 nt) | rluA1 | pseudouridylate synthase | |||||
| * | ? | CP000730 | 1226920 = | 45 (1.080) | 3 (0.080) | 3/240 | NT | 7.4% | intergenic (+53/‑612) | USA300HOU_1151/def2 | hypothetical lipoprotein/formylmethionine deformylase |
| ? | CP000730 | 1227017 = | 33 (0.850) | intergenic (+150/‑515) | USA300HOU_1151/def2 | hypothetical lipoprotein/formylmethionine deformylase | |||||
| * | ? | CP000730 | 1234260 = | 47 (1.130) | 3 (0.080) | 3/240 | NT | 6.7% | intergenic (+170/‑58) | prkC/engC | non‑specific serine/threonine protein kinase/possible GTP‑binding protein EngC |
| ? | CP000730 | 1234304 = | 40 (1.030) | intergenic (+214/‑14) | prkC/engC | non‑specific serine/threonine protein kinase/possible GTP‑binding protein EngC | |||||
| * | ? | CP000730 | = 1653774 | 33 (0.790) | 3 (0.070) | 3/252 | NT | 8.5% | coding (205/525 nt) | aroK | shikimate kinase |
| ? | CP000730 | = 1653820 | 32 (0.790) | coding (159/525 nt) | aroK | shikimate kinase | |||||
| * | ? | CP000730 | 1697752 = | 37 (0.890) | 3 (0.080) | 3/226 | NT | 9.0% | intergenic (+8/+37) | rpsT/holA | ribosomal protein S20/possible DNA‑directed DNA polymerase III delta subunit |
| ? | CP000730 | 1697788 = | 28 (0.770) | intergenic (+44/+1) | rpsT/holA | ribosomal protein S20/possible DNA‑directed DNA polymerase III delta subunit | |||||
| * | ? | CP000730 | = 1903775 | 35 (0.840) | 2 (0.060) | 3/222 | NT | 5.6% | intergenic (+229/+66) | arsC2/gad | arsenate reductase (glutaredoxin)/possible mannosyl‑glycoprotein endo‑beta‑N‑glucosaminidase |
| ? | CP000730 | = 1903782 | 37 (1.030) | intergenic (+236/+59) | arsC2/gad | arsenate reductase (glutaredoxin)/possible mannosyl‑glycoprotein endo‑beta‑N‑glucosaminidase | |||||
| * | ? | CP000730 | 1929987 = | 30 (0.720) | 3 (0.080) | 3/232 | NT | 10.0% | intergenic (‑1070/‑98) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| ? | CP000730 | 1930020 = | 27 (0.720) | intergenic (‑1103/‑65) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000730 | 2249230 = | 46 (1.100) | 3 (0.080) | 3/244 | NT | 6.6% | intergenic (‑223/+176) | USA300HOU_2120/USA300HOU_2121 | hypothetical protein/hypothetical protein |
| ? | CP000730 | 2249273 = | 41 (1.040) | intergenic (‑266/+133) | USA300HOU_2120/USA300HOU_2121 | hypothetical protein/hypothetical protein | |||||