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 | annotation | gene | description |
| RA | 478,502 | C→A | D342E (GAC→GAA) | ndhF → | NADH dehydrogenase (ubiquinone) |
| RA | 584,121 | G→T | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 707,909 | A→T | M1M (TTG→ATG) † | mntB ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 973,213 | C→A | E175* (GAG→TAG) | yitU ← | possible HAD superfamily hydrolase |
| RA | 1,002,200 | T→G | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,105,994 | T→C | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,196,508 | C→A | intergenic (+2563/‑1229) | ftsQ → / → ylmE | cell division protein FtsQ/hypothetical protein |
| RA | 1,232,053 | A→T | D233V (GAT→GTT) | prpC → | possible PP2C protein phosphatase |
| RA | 1,416,458 | A→T | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,646,189 | G→C | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,473 | C→T | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 2,002,518 | T→C | noncoding (896/1540 nt) | rrs3 ← | 16S ribosomal RNA |
| RA | 2,010,363 | C→T | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,279,705 | G→A | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,289,257 | A→C | V78G (GTA→GGA) | ybbP ← | hypothetical membrane protein |
| RA | 2,337,959 | C→T | intergenic (‑125/‑119) | adhR ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,455,692 | Δ1 bp | coding (1210/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,698 | 2 bp→AT | coding (1216‑1217/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,532,298 | A→T | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP000730 | 58367 | 58581 | 215 | 2 [1] | [1] 2 | [USA300HOU_0049] | [USA300HOU_0049] |
| * | * | ÷ | CP000730 | 58810 | 58989 | 180 | 2 [1] | [1] 2 | USA300HOU_0049/USA300HOU_0050 | hypothetical protein/hypothetical protein |
| * | * | ÷ | CP000730 | 85126 | 85218 | 93 | 2 [1] | [1] 2 | USA300HOU_0082/copB | nickel (Ni2+)/peptide ABC superfamily ATP binding cassette transporter, ABC protein/P‑ATPase superfamily P‑type ATPase copper (Cu2+) transporter |
| * | * | ÷ | CP000730 | 170875 | 170903 | 29 | 3 [1] | [1] 2 | USA300HOU_0160/adhE | hypothetical protein/alcohol dehydrogenase |
| * | * | ÷ | CP000730 | 611529 | 611623 | 95 | 3 [1] | [1] 2 | azo1/sdrC | hypothetical protein/Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrC |
| * | * | ÷ | CP000730 | 661200 | 661313 | 114 | 2 [1] | [0] 2 | USA300HOU_0602 | hypothetical protein |
| * | * | ÷ | CP000730 | 662708 | 662817 | 110 | 2 [1] | [1] 2 | USA300HOU_0605 | hypothetical protein |
| * | * | ÷ | CP000730 | 742725 | 742840 | 116 | 2 [1] | [1] 2 | yetJ/sarX | hypothetical membrane protein/possible staphylococcal accessory protein X |
| * | * | ÷ | CP000730 | 760815 | 760839 | 25 | 2 [0] | [1] 2 | [cobW2] | [cobW2] |
| * | * | ÷ | CP000730 | 1164471 | 1164570 | 100 | 3 [1] | [1] 2 | USA300HOU_1089/USA300HOU_1090 | hypothetical protein/hypothetical protein |
| * | * | ÷ | CP000730 | 1171580 | 1171700 | 121 | 2 [1] | [1] 2 | hly/USA300HOU_1100 | alpha‑hemolysin/hypothetical protein |
| * | * | ÷ | CP000730 | 1181503 | 1181602 | 100 | 3 [1] | [1] 2 | USA300HOU_1111/USA300HOU_t0016 | hypothetical protein/tRNA‑Arg |
| * | * | ÷ | CP000730 | 1295723 | 1295851 | 129 | 2 [1] | [1] 2 | rpsO/pnp | ribosomal protein S15/polyribonucleotide nucleotidyltransferase |
| * | * | ÷ | CP000730 | 1604524 | 1604655 | 132 | 2 [1] | [1] 2 | [USA300HOU_1489] | [USA300HOU_1489] |
| * | * | ÷ | CP000730 | 1885309 | 1885367 | 59 | 2 [1] | [1] 2 | fmtB1/USA300HOU_1748 | cell surface anchored protein/possible rhodanese domain sulfurtransferase |
| * | * | ÷ | CP000730 | 1934817 | 1934921 | 105 | 3 [1] | [1] 2 | USA300HOU_1798 | hypothetical protein |
| * | * | ÷ | CP000730 | 1960897 | 1960980 | 84 | 2 [1] | [1] 2 | USA300HOU_1820/USA300HOU_1821 | hypothetical bacteriophage protein/hypothetical protein |
| * | * | ÷ | CP000730 | 2055594 | 2055697 | 104 | 4 [1] | [1] 2 | purB/sspP | adenylosuccinate lyase/C47 family staphopain protease |
| * | * | ÷ | CP000730 | 2507013 | 2507105 | 93 | 2 [1] | [1] 3 | USA300HOU_2367/sarZ | hypothetical protein/transcriptional regulator |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 16 (0.230) | 38 (0.750) +40 bp |
32/220 | 0.3 | 76.4% | 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 | = 514218 | NA (NA) | 4 (0.060) | 4/290 | 2.1 | NA | noncoding (1426/1540 nt) | rrs1 | 16S ribosomal RNA |
| ? | CP000730 | = 514270 | NA (NA) | noncoding (1478/1540 nt) | rrs1 | 16S ribosomal RNA | |||||
| * | ? | CP000730 | = 515946 | NA (NA) | 3 (0.050) | 3/286 | 2.3 | NA | noncoding (1241/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | = 515981 | NA (NA) | noncoding (1276/2921 nt) | rrl1 | 23S ribosomal RNA | |||||
| * | ? | CP000730 | = 517446 | NA (NA) | 10 (0.150) | 6/286 | 1.8 | NA | noncoding (2741/2921 nt) | rrl1 | 23S ribosomal RNA |
| ? | CP000730 | = 517450 | NA (NA) | noncoding (2745/2921 nt) | rrl1 | 23S ribosomal RNA | |||||
| * | ? | CP000730 | = 2002534 | 12 (0.170) | 90 (2.110) +57 bp |
48/186 | 0.1 | 92.4% | noncoding (880/1540 nt) | rrs3 | 16S ribosomal RNA |
| ? | CP000730 | 2002593 = | NA (NA) | noncoding (821/1540 nt) | rrs3 | 16S ribosomal RNA | |||||