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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 5,952 | C→T | 10.6% | R298C (CGT→TGT) | gyrB → | DNA topoisomerase (ATP‑hydrolyzing) subunit B |
| RA | 9,710 | T→C | 5.1% | intergenic (+15/+72) | gyrA → / ← nnrD | DNA topoisomerase (ATP‑hydrolyzing) subunit A/possible carbohydrate kinase |
| RA | 9,716 | T→C | 5.1% | intergenic (+21/+66) | gyrA → / ← nnrD | DNA topoisomerase (ATP‑hydrolyzing) subunit A/possible carbohydrate kinase |
| RA | 9,725 | G→A | 5.0% | intergenic (+30/+57) | gyrA → / ← nnrD | DNA topoisomerase (ATP‑hydrolyzing) subunit A/possible carbohydrate kinase |
| 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 | 41,166 | G→A | 5.8% | intergenic (‑33/‑139) | mecA ← / → mecR1 | penicillin binding protein 2 prime/methicillin resistance regulatory protein MecR1 |
| RA | 41,171 | T→C | 8.0% | intergenic (‑38/‑134) | mecA ← / → mecR1 | penicillin binding protein 2 prime/methicillin resistance regulatory protein MecR1 |
| RA | 50,709 | Δ1 bp | 100% | coding (204/1788 nt) | cch ← | hypothetical protein |
| RA | 97,167 | G→T | 7.3% | intergenic (‑103/+196) | USA300HOU_0095 ← / ← dus | hypothetical protein/possible tRNA‑dihydrouridine synthase |
| RA | 110,651 | C→T | 11.7% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 19.0% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,904 | G→T | 41.3% | D255Y (GAT→TAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,329 | T→A | 9.3% | N133K (AAT→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 38.3% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 37.6% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 19.3% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,572 | C→T | 8.2% | D214D (GAC→GAT) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 119,853 | C→A | 57.2% | G254W (GGG→TGG) | yjbB ← | possible PnaS family phosphate:sodium (Na+) symporter |
| RA | 253,983 | A→G | 7.9% | R3R (AGA→AGG) | USA300HOU_0227 → | hypothetical protein |
| RA | 253,984 | G→T | 8.5% | V4L (GTA→TTA) | USA300HOU_0227 → | hypothetical protein |
| RA | 255,394 | A→T | 5.6% | I179I (ATA→ATT) | glpT → | MFS family major facilitator transporter, hexose phosphate:cation symporter |
| RA | 328,487 | C→A | 8.6% | I210I (ATC→ATA) | USA300HOU_0294 → | hypothetical membrane protein |
| RA | 443,935 | G→T | 5.1% | intergenic (‑235/+26) | USA300HOU_0417 ← / ← USA300HOU_0419 | transposase/hypothetical protein |
| RA | 478,502 | C→A | 100% | D342E (GAC→GAA) | ndhF → | NADH dehydrogenase (ubiquinone) |
| RA | 492,848 | A→T | 7.6% | F62Y (TTC→TAC) | USA300HOU_0466 ← | hypothetical protein |
| RA | 503,565 | G→A | 8.4% | noncoding (20/93 nt) | USA300HOU_t0003 → | tRNA‑Ser |
| RA | 512,643 | A→G | 45.4% | 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 | 589,532 | G→T | 8.4% | D1146Y (GAT→TAT) ‡ | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | 589,533 | A→T | 9.0% | D1146V (GAT→GTT) ‡ | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | 618,588 | G→A | 9.0% | S1230S (TCG→TCA) | sdrD → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD |
| RA | 618,759 | T→C | 11.1% | D1287D (GAT→GAC) | sdrD → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD |
| RA | 622,464 | G→A | 11.8% | S1009S (TCG→TCA) | sdrE → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrE |
| RA | 631,535 | G→A | 5.6% | intergenic (+161/‑341) | USA300HOU_0566 → / → proP | possible phosphatase/MFS family major facilitator transporter, proline/betaine:cation symporter |
| RA | 707,909 | A→T | 100% | M1M (TTG→ATG) † | mntB ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 740,315 | Δ1 bp | 5.4% | intergenic (+542/+46) | pitA → / ← sle1 | possible PiT family inorganic phosphate transporter/possible LysM domain protein |
| RA | 779,970 | G→A | 6.4% | intergenic (+26/+46) | csbB → / ← saeS | possible glycosyltransferase/sensor histidine kinase SaeS |
| RA | 849,656 | G→A | 57.4% | G261D (GGT→GAT) | yvcJ → | ATP‑binding protein |
| RA | 937,158 | T→A | 6.4% | intergenic (+65/‑1952) | yumB → / → USA300HOU_0903 | NADH dehydrogenase/NhaC family sodium:proton (Na+:H+) antiporter |
| 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 | 1,105,994 | 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 | 1,218,730 | G→T | 5.9% | intergenic (+221/+42) | USA300HOU_1145 → / ← fbpA | possible 3‑demethylubiquinone‑9 3‑methyltransferase/fibrinogen‑binding protein |
| RA | 1,218,732 | C→G | 6.8% | intergenic (+223/+40) | USA300HOU_1145 → / ← fbpA | possible 3‑demethylubiquinone‑9 3‑methyltransferase/fibrinogen‑binding protein |
| RA | 1,218,734 | A→C | 5.1% | intergenic (+225/+38) | USA300HOU_1145 → / ← fbpA | possible 3‑demethylubiquinone‑9 3‑methyltransferase/fibrinogen‑binding protein |
| RA | 1,231,411 | A→G | 100% | D19G (GAT→GGT) | prpC → | possible PP2C protein phosphatase |
| JC | 1,333,784 | 30 bp→30 bp | 12.9% | coding (185‑214/1239 nt) | hflX → | GTP‑binding protein |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,500,441 | A→T | 5.1% | L528Q (CTA→CAA) | 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 | 22.6% | 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 | 56.1% | coding (2073‑2075/2280 nt) | secDF ← | RND superfamily resistance‑nodulation‑cell division protein:proton (H+) antiporter |
| RA | 1,857,867 | C→T | 17.3% | L169L (TTG→TTA) | USA300HOU_1728 ← | hypothetical protein |
| RA | 1,909,214 | C→A | 45.4% | Y7* (TAC→TAA) | USA300HOU_1771 → | hypothetical membrane protein |
| RA | 1,931,599 | A→T | 6.6% | L1217I (TTA→ATA) | USA300HOU_1798 ← | hypothetical 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 | 2,172,075 | G→C | 7.1% | E42Q (GAA→CAA) | leuB → | 3‑isopropylmalate dehydrogenase |
| RA | 2,172,078 | T→A | 7.3% | F43I (TTT→ATT) | leuB → | 3‑isopropylmalate dehydrogenase |
| RA | 2,172,081 | G→C | 7.3% | G44R (GGT→CGT) | leuB → | 3‑isopropylmalate dehydrogenase |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,283,586 | A→T | 5.3% | intergenic (+5254/+2778) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,291,888 | G→A | 7.4% | K359K (AAG→AAA) | USA300HOU_2155 → | transposase |
| 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 | 48.5% | R239H (CGT→CAT) | secY1 ← | Sec family Type I general secretory pathway preprotein translocase SecY |
| RA | 2,444,869 | T→A | 5.7% | L15F (TTA→TTT) | USA300HOU_2306 ← | NhaC family sodium:proton (Na+:H) antiporter |
| 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 | 2,504,989 | T→C | 8.7% | intergenic (+293/+111) | USA300HOU_2365 → / ← gltT | hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,624,242 | C→T | 5.9% | intergenic (‑1572/+2464) | USA300HOU_2485 ← / ← sarT | MFS family major facilitator transporter, cation symporter/staphylococcal accessory regulator T |
| RA | 2,627,280 | T→A | 6.3% | intergenic (‑215/‑107) | sarT ← / → sarU | staphylococcal accessory regulator T/staphylococcal accessory regulator U |
| RA | 2,696,558 | T→C | 5.3% | intergenic (+110/‑130) | USA300HOU_2551 → / → copA | hypothetical protein/P‑ATPase superfamily P‑type ATPase copper (Cu2+) transporter |
| RA | 2,774,981 | A→G | 7.9% | D735D (GAT→GAC) | clfB ← | clumping factor B |
| RA | 2,775,029 | G→A | 6.3% | D719D (GAC→GAT) | clfB ← | clumping factor B |
| RA | 2,775,041 | A→G | 8.5% | D715D (GAT→GAC) | clfB ← | clumping factor B |
| RA | 2,775,053 | A→G | 6.1% | D711D (GAT→GAC) | clfB ← | clumping factor B |
| RA | 2,846,695 | A→G | 5.2% | V34V (GTT→GTC) | cbiQ ← | hypothetical protein |
| RA | 2,854,538 | T→A | 5.9% | intergenic (+236/+177) | 2486 → / ← rarD | DASS family divalent anion:sodium (Na+) symporter/DMT superfamily drug/metabolite transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 34173 = | 92 (0.930) | 11 (0.120) | 11/246 | NT | 9.9% | coding (462/480 nt) | orfX | hypothetical protein OrfX |
| ? | CP000730 | = 57858 | 113 (1.200) | intergenic (+304/+613) | USA300HOU_0048/USA300HOU_0049 | hypothetical membrane protein/hypothetical protein | |||||
| * | ? | CP000730 | 52495 = | 94 (0.950) | 143 (1.450) +T |
5/256 | NT | 58.0% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 115 (1.160) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 512620 = | 138 (1.390) | 72 (1.060) +40 bp |
54/178 | NT | 43.1% | 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 | 513404 = | NA (NA) | 7 (0.070) | 5/246 | NT | NA | noncoding (612/1540 nt) | rrs1 | 16S ribosomal RNA |
| ? | CP000730 | 513421 = | NA (NA) | noncoding (629/1540 nt) | rrs1 | 16S ribosomal RNA | |||||
| * | ? | CP000730 | = 516433 | NA (NA) | 3 (0.030) | 3/248 | NT | NA | noncoding (1728/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | = 516448 | NA (NA) | noncoding (1743/2921 nt) | rrl1 | 23S ribosomal RNA | |||||
| * | ? | CP000730 | 528464 = | 76 (0.770) | 4 (0.050) | 3/230 | NT | 5.6% | intergenic (+5/‑162) | tatD/rnmV | TatD family deoxyribonuclease/hypothetical protein |
| ? | CP000730 | 528541 = | 68 (0.770) | intergenic (+82/‑85) | tatD/rnmV | TatD family deoxyribonuclease/hypothetical protein | |||||
| * | ? | CP000730 | = 528477 | 79 (0.800) | 4 (0.050) | 4/230 | NT | 5.5% | intergenic (+18/‑149) | tatD/rnmV | TatD family deoxyribonuclease/hypothetical protein |
| ? | CP000730 | = 528526 | 68 (0.770) | intergenic (+67/‑100) | tatD/rnmV | TatD family deoxyribonuclease/hypothetical protein | |||||
| * | ? | CP000730 | = 557256 | NA (NA) | 6 (0.070) | 6/240 | NT | NA | noncoding (185/1540 nt) | rrs2 | 16S ribosomal RNA |
| ? | CP000730 | = 557260 | NA (NA) | noncoding (189/1540 nt) | rrs2 | 16S ribosomal RNA | |||||
| * | ? | CP000730 | 854380 = | 84 (0.850) | 7 (0.070) | 6/246 | NT | 8.1% | intergenic (‑242/‑460) | USA300HOU_0798/USA300HOU_0799 | nucleoside‑diphosphate sugar epimerase/hypothetical protein |
| ? | CP000730 | 854405 = | 79 (0.840) | intergenic (‑267/‑435) | USA300HOU_0798/USA300HOU_0799 | nucleoside‑diphosphate sugar epimerase/hypothetical protein | |||||
| * | ? | CP000730 | 1084754 = | 80 (0.810) | 4 (0.040) | 3/238 | NT | 5.1% | intergenic (+126/+139) | purD/USA300HOU_1019 | phosphoribosylamine‑‑glycine ligase/ABC superfamily ATP binding cassette transporter, membrane protein |
| ? | CP000730 | 1084817 = | 74 (0.810) | intergenic (+189/+76) | purD/USA300HOU_1019 | phosphoribosylamine‑‑glycine ligase/ABC superfamily ATP binding cassette transporter, membrane protein | |||||
| * | ? | CP000730 | = 1443583 | 78 (0.790) | 4 (0.040) | 3/248 | NT | 7.2% | intergenic (‑156/+197) | USA300HOU_1341/brnQ2 | IS1272 transposase/LIVCS family branched chain amino acid:cation symporter |
| ? | CP000730 | 2317554 = | 28 (0.290) | intergenic (+207/+1909) | rhbC/asp23 | possible Iuc family aerobactin synthesis protein/alkaline shock protein 23 | |||||
| * | ? | CP000730 | 2179606 = | NA (NA) | 4 (0.040) | 4/244 | NT | 100% | intergenic (‑50/+262) | rrl4/rrs4 | 23S ribosomal RNA/16S ribosomal RNA |
| ? | CP000730 | 2179610 = | 0 (0.000) | intergenic (‑54/+258) | rrl4/rrs4 | 23S ribosomal RNA/16S ribosomal RNA | |||||
| * | ? | CP000730 | 2388283 = | 110 (1.110) | 6 (0.070) | 6/224 | NT | 6.6% | intergenic (+18/+84) | USA300HOU_2247/USA300HOU_2248 | MFS family major facilitator transporter/hypothetical protein |
| ? | CP000730 | 2388362 = | 74 (0.860) | intergenic (+97/+5) | USA300HOU_2247/USA300HOU_2248 | MFS family major facilitator transporter/hypothetical protein | |||||
| * | ? | CP000730 | 2693368 = | 85 (0.860) | 6 (0.070) | 5/234 | NT | 7.6% | intergenic (+39/+38) | USA300HOU_2547/USA300HOU_2548 | TetR family transcriptional regulator/hypothetical protein |
| ? | CP000730 | 2693417 = | 69 (0.770) | coding (157/168 nt) | USA300HOU_2548 | hypothetical protein | |||||