mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 19,264 | G→A | 27.8% | G307D (GGC→GAC) | USA300HOU_0014 → | DHH subfamily phosphodiesterase |
| RA | 19,294 | C→T | 48.6% | T317I (ACT→ATT) | USA300HOU_0014 → | DHH subfamily phosphodiesterase |
| RA | 36,087 | A→G | 4.5% | C155C (TGT→TGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 37,539 | C→A | 21.5% | intergenic (+235/‑274) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,540 | A→G | 17.8% | intergenic (+236/‑273) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,542 | T→C | 18.9% | intergenic (+238/‑271) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,551 | T→A | 40.8% | intergenic (+247/‑262) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,558 | G→A | 51.2% | intergenic (+254/‑255) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,562 | A→G | 60.7% | intergenic (+258/‑251) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,563 | A→C | 60.6% | intergenic (+259/‑250) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,574 | A→G | 66.8% | intergenic (+270/‑239) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,576 | C→T | 67.6% | intergenic (+272/‑237) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,579 | A→C | 65.6% | intergenic (+275/‑234) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 37,591 | A→T | 66.1% | intergenic (+287/‑222) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 38,688 | C→A | 8.7% | F12L (TTC→TTA) | maoC → | possible acyl dehydratase MaoC |
| RA | 39,378 | C→T | 75.7% | D586N (GAT→AAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 39,672 | C→A | 29.3% | V488F (GTT→TTT) | mecA ← | penicillin binding protein 2 prime |
| RA | 76,969 | G→A | 32.0% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 9.7% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 11.9% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 28.3% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 27.2% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 6.4% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 195,286 | T→A | 23.3% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 279,564 | C→T | 3.8% | G211S (GGC→AGC) | USA300HOU_0246 ← | ABC superfamily ATP binding cassette transporter, binding protein |
| RA | 383,775 | C→T | 3.1% | T44T (ACG→ACA) | USA300HOU_0350 ← | PTS family porter component IIC |
| RA | 396,540 | G→A | 25.9% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 442,222 | A→G | 5.6% | intergenic (‑290/+103) | USA300HOU_0415 ← / ← USA300HOU_0416 | hypothetical protein/hypothetical protein |
| RA | 478,502 | C→A | 70.7% | D342E (GAC→GAA) | USA300HOU_0457 → | NADH dehydrogenase (ubiquinone) |
| RA | 512,643 | A→G | 58.4% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 512,721 | C→A | 4.3% | intergenic (+789/‑72) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 584,121 | G→T | 77.5% | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 588,312 | A→G | 3.2% | E739G (GAG→GGG) | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | 602,827 | T→C | 3.8% | G87G (GGT→GGC) | araB → | ribulokinase |
| RA | 607,884 | G→A | 31.1% | R209* (CGA→TGA) | USA300HOU_0550 ← | deoxynucleoside kinase |
| RA | 629,681 | C→A | 27.9% | L84I (CTA→ATA) | USA300HOU_0564 → | possible 3‑hexulose‑6‑phosphate synthase |
| RA | 665,326 | T→A | 3.0% | L57* (TTA→TAA) | USA300HOU_0608 → | possible acetytransferase |
| RA | 665,392 | T→G | 19.4% | L79* (TTA→TGA) | USA300HOU_0608 → | possible acetytransferase |
| RA | 694,071 | G→T | 14.4% | A50E (GCA→GAA) | USA300HOU_0638 ← | hypothetical protein |
| RA | 707,909 | A→T | 69.5% | M1M (TTG→ATG) † | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 707,910 | A→G | 31.3% | intergenic (‑1/‑121) | USA300HOU_0653 ← / → USA300HOU_0654 | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 772,803 | C→A | 6.1% | A18E (GCA→GAA) | fruA → | PTS family fructose/mannitol (fru) porter component IIABC |
| RA | 804,673 | A→T | 26.3% | L135I (TTA→ATA) | USA300HOU_0751 ← | POT family proton (H+)‑dependent oligopeptide transporter |
| RA | 828,298 | T→A | 8.2% | intergenic (+213/‑151) | USA300HOU_0776 → / → USA300HOU_0777 | hypothetical protein/possible superfamily II DNA/RNA helicase ComFA |
| RA | 829,785 | A→G | 3.4% | K89E (AAA→GAA) | USA300HOU_0778 → | possible superfamily II DNA/RNA helicase ComFC |
| RA | 864,745 | C→G | 6.6% | L21V (CTA→GTA) | USA300HOU_0809 → | carboxylesterase |
| RA | 973,213 | C→A | 72.2% | E175* (GAG→TAG) | USA300HOU_0930 ← | possible HAD superfamily hydrolase |
| RA | 1,002,200 | T→G | 77.7% | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,064,445 | Δ1 bp | 27.3% | coding (44/1218 nt) | USA300HOU_1000 ← | LytR family transcriptional regulator |
| RA | 1,067,178 | A→G | 4.1% | S128S (TCT→TCC) | qoxC ← | quinol oxidase subunit III |
| RA | 1,070,777 | T→A | 4.8% | intergenic (‑138/‑164) | qoxA ← / → USA300HOU_1006 | quinol oxidase subunit II/hypothetical protein |
| RA | 1,105,994 | T→C | 69.2% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,146,228 | A→G | 3.6% | E92G (GAA→GGA) | pheS → | phenylalanine‑‑tRNA ligase alpha subunit |
| RA | 1,151,773 | T→C | 5.1% | I7T (ATC→ACC) | dinB → | DNA‑directed DNA polymerase IV beta subunit |
| RA | 1,174,980 | T→C | 4.3% | A36A (GCA→GCG) | USA300HOU_1105 ← | exotoxin |
| RA | 1,196,508 | C→A | 62.1% | intergenic (+2563/‑1229) | ftsQ → / → USA300HOU_1125 | cell division protein FtsQ/hypothetical protein |
| RA | 1,231,470 | A→C | 7.5% | M39L (ATG→CTG) | USA300HOU_1156 → | possible PP2C protein phosphatase |
| RA | 1,232,148 | G→C | 68.1% | G18A (GGC→GCC) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,233,504 | T→A | 30.8% | V470D (GTT→GAT) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,266,747 | C→A | 4.8% | P13T (CCT→ACT) | topA → | DNA topoisomerase A |
| RA | 1,311,043 | G→T | 4.1% | E302* (GAA→TAA) | recA → | recombination protein RecA |
| RA | 1,415,237 | T→A | 5.0% | I92L (ATA→TTA) | USA300HOU_1312 ← | hypothetical protein |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,440,085 | G→T | 39.5% | intergenic (‑45/‑891) | cspA ← / → xpaC | cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,539,250 | C→G | 64.8% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_1405 | chorismate synthase/hypothetical protein |
| RA | 1,551,935 | G→T | 5.6% | S180* (TCA→TAA) | ebpS ← | elastin‑binding protein |
| RA | 1,577,317 | A→T | 9.4% | V67D (GTT→GAT) | USA300HOU_1441 ← | possible bacteriophage tail protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,653,550 | A→G | 4.2% | N143N (AAT→AAC) | aroK ← | shikimate kinase |
| RA | 1,744,362 | G→A | 20.9% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,473 | C→T | 70.7% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,749,331 | C→A | 35.6% | G40C (GGT→TGT) | secDF ← | RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter |
| RA | 1,761,889 | C→A | 17.4% | D388Y (GAT→TAT) | folC ← | tetrahydrofolate synthase |
| RA | 1,776,265 | C→A | 10.9% | V87L (GTA→TTA) | clpX ← | S14 family endopeptidase ClpX |
| RA | 1,808,702 | A→T | 6.7% | I204I (ATT→ATA) | accA ← | acetyl‑CoA carboxylase alpha subunit |
| RA | 1,837,203 | G→T | 7.7% | Q332K (CAA→AAA) | USA300HOU_1714 ← | hypothetical protein |
| RA | 1,912,184 | T→G | 32.2% | intergenic (+1717/+366) | USA300HOU_1773 → / ← USA300HOU_1775 | camphor resistance protein/possible aldo/keto reductase |
| RA | 1,963,768 | C→G | 23.5% | V365L (GTA→CTA) | hemG ← | protoporphyrinogen oxidase |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,028,394 | A→C | 68.3% | F84C (TTT→TGT) | USA300HOU_1882 ← | hypothetical membrane protein |
| RA | 2,028,583 | G→T | 24.9% | A21D (GCC→GAC) | USA300HOU_1882 ← | hypothetical membrane protein |
| RA | 2,105,002 | A→T | 6.5% | L70* (TTA→TAA) | USA300HOU_1967 ← | hypothetical bacteriophage protein |
| RA | 2,123,847 | T→A | 7.7% | intergenic (‑107/‑26) | USA300HOU_2003 ← / → USA300HOU_2004 | possible transcriptional regulator/possible bifunctional S24 family peptidase/transcriptional regulator |
| 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 | 71.8% | intergenic (‑125/‑119) | USA300HOU_2195 ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,352,815 | G→A | 27.5% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,454,626 | A→T | 30.2% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,692 | Δ1 bp | 59.4% | coding (1210/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,698 | C→A | 100% | H406N (CAT→AAT) ‡ | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,699 | A→T | 68.4% | H406L (CAT→CTT) ‡ | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,542,325 | G→T | 70.2% | A29S (GCC→TCC) | hlgA → | gamma‑hemolysin component A |
| RA | 2,562,956 | A→C | 7.2% | I211L (ATT→CTT) | USA300HOU_2424 → | APC family amino acid‑polyamine‑organocation transporter |
| RA | 2,571,957 | A→G | 4.1% | intergenic (‑109/+117) | panE1 ← / ← USA300HOU_2433 | 2‑dehydropantoate 2‑reductase/MFS family major facilitator transporter |
| RA | 2,774,846 | A→G | 13.2% | S780S (AGT→AGC) | clfB ← | clumping factor B |
| RA | 2,818,647 | A→G | 2.9% | intergenic (‑319/+226) | USA300HOU_2654 ← / ← USA300HOU_2655 | serine‑threonine rich protein/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 85 (0.820) | 86 (1.210) +40 bp |
59/180 | NT | 59.5% | 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 | = 782423 | 79 (0.770) | 3 (0.030) | 3/240 | NT | 3.8% | intergenic (‑218/+124) | USA300HOU_0730/USA300HOU_0731 | hypothetical membrane protein/hypothetical lipoprotein |
| ? | CP000730 | = 782442 | 79 (0.830) | intergenic (‑237/+105) | USA300HOU_0730/USA300HOU_0731 | hypothetical membrane protein/hypothetical lipoprotein | |||||
| * | ? | CP000730 | = 800928 | 92 (0.890) | 9 (0.090) | 8/246 | NT | 8.1% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 116 (1.190) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||
| * | ? | CP000730 | = 810093 | 122 (1.180) | 3 (0.030) | 3/246 | NT | 2.6% | intergenic (+24/‑94) | nrdE/nrdF | ribonuceloside diphosphate reductase subunit alpha/ribonucleoside‑diphosphate reductase subunit beta |
| ? | CP000730 | = 810144 | 107 (1.100) | intergenic (+75/‑43) | nrdE/nrdF | ribonuceloside diphosphate reductase subunit alpha/ribonucleoside‑diphosphate reductase subunit beta | |||||
| * | ? | CP000730 | 864131 = | 93 (0.900) | 4 (0.040) | 3/254 | NT | 4.1% | coding (321/459 nt) | USA300HOU_0807 | hypothetical membrane protein |
| ? | CP000730 | 864198 = | 94 (0.930) | coding (388/459 nt) | USA300HOU_0807 | hypothetical membrane protein | |||||
| * | ? | CP000730 | 1131177 = | 111 (1.080) | 4 (0.040) | 3/242 | NT | 3.7% | intergenic (+141/‑1087) | USA300HOU_1058/USA300HOU_1059 | hypothetical protein/hypothetical protein |
| ? | CP000730 | 1131203 = | 103 (1.070) | intergenic (+167/‑1061) | USA300HOU_1058/USA300HOU_1059 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000730 | 1343877 = | 83 (0.800) | 3 (0.030) | 3/248 | NT | 3.9% | coding (14/267 nt) | USA300HOU_1252 | hypothetical protein |
| ? | CP000730 | 1343895 = | 69 (0.700) | coding (32/267 nt) | USA300HOU_1252 | hypothetical protein | |||||
| * | ? | CP000730 | = 1744053 | 92 (0.890) | 3 (0.030) | 3/246 | NT | 3.6% | intergenic (‑307/+100) | relA2/apt | GTP pyrophosphokinase/adenine phosphoribosyltransferase |
| ? | CP000730 | = 1744121 | 75 (0.770) | intergenic (‑375/+32) | relA2/apt | GTP pyrophosphokinase/adenine phosphoribosyltransferase | |||||
| * | ? | CP000730 | 2257232 = | 83 (0.800) | 4 (0.040) | 3/248 | NT | 5.0% | coding (293/414 nt) | USA300HOU_2129 | hypothetical protein |
| ? | CP000730 | 2257282 = | 74 (0.750) | coding (243/414 nt) | USA300HOU_2129 | hypothetical protein | |||||