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 | annotation | gene | description |
| RA | 36,378 | C→T | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 39,195 | T→C | K647E (AAA→GAA) | mecA ← | penicillin binding protein 2 prime |
| RA | 39,378 | C→T | D586N (GAT→AAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 51,334 | (G)7→8 | coding (36/1092 nt) | USA300HOU_0043 → | hypothetical membrane protein |
| RA | 76,969 | G→A | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 93,268 | G→A | A73T (GCT→ACT) | yrkE → | hypothetical protein |
| RA | 129,796 | G→C | intergenic (‑173/+212) | spa ← / ← sarH1 | immunoglobulin G binding protein A/staphylococcal accessory regulator H1 |
| RA | 169,407 | G→A | intergenic (+1374/‑130) | USA300HOU_0157 → / → USA300HOU_0160 | nucleotidase/hypothetical protein |
| RA | 195,286 | T→A | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 266,981 | A→G | P228P (CCA→CCG) | USA300HOU_0238 → | staphylocoagulase |
| RA | 396,540 | G→A | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 505,514 | C→T | A469V (GCG→GTG) | treP → | PTS family trehalose (tre) porter component IIBC |
| RA | 536,758 | C→T | P202L (CCA→CTA) | rplY → | ribosomal protein L25 |
| RA | 607,884 | G→A | R209* (CGA→TGA) | dck ← | deoxynucleoside kinase |
| RA | 629,681 | C→A | L84I (CTA→ATA) | hxlA → | possible 3‑hexulose‑6‑phosphate synthase |
| RA | 665,392 | T→G | L79* (TTA→TGA) | iolS → | possible acetytransferase |
| RA | 707,910 | A→G | intergenic (‑1/‑121) | mntB ← / → sirR | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 744,375 | A→T | intergenic (+2212/‑714) | yetJ → / → sarX | hypothetical membrane protein/possible staphylococcal accessory protein X |
| RA | 749,249 | C→T | S59S (AGC→AGT) | USA300HOU_0696 → | MFS family major facilitator transporter, sugar:cation symporter |
| RA | 890,260 | T→C | V39A (GTT→GCT) | gcvH → | glycine cleavage system protein H |
| RA | 1,017,678 | T→C | F391S (TTC→TCC) | USA300HOU_0971 → | AGCS family alanine or glycine:sodium (Na+) or proton (H+) symporter |
| RA | 1,063,912 | +C | coding (577/1218 nt) | brpA ← | LytR family transcriptional regulator |
| RA | 1,125,066 | G→C | E729Q (GAG→CAG) | pycA → | pyruvate carboxylase |
| RA | 1,163,829 | T→C | V72A (GTG→GCG) | ysnB → | hypothetical protein |
| RA | 1,233,504 | T→A | V470D (GTT→GAT) | prkC → | non‑specific serine/threonine protein kinase |
| RA | 1,298,108 | T→A | intergenic (+4/‑232) | pnp → / → rnjB | polyribonucleotide nucleotidyltransferase/beta‑lactamase |
| RA | 1,324,256 | (A)9→8 | coding (1028/2010 nt) | mutL → | DNA mismatch repair protein MutL |
| RA | 1,358,236 | A→G | G300G (GGA→GGG) | thrA → | homoserine dehydrogenase |
| RA | 1,416,458 | A→T | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,440,085 | G→T | intergenic (‑45/‑891) | cspA ← / → xpaC | cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC |
| RA | 1,499,376 | C→A | G883V (GGT→GTT) | ebh ← | extracellular matrix binding protein |
| RA | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,613,762 | T→C | intergenic (‑31/‑37) | scpA ← / → USA300HOU_1497 | possible segregation and condensation protein A/hypothetical protein |
| RA | 1,624,673 | T→A | K192I (AAA→ATA) | malA ← | alpha‑glucosidase |
| RA | 1,646,189 | G→C | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,362 | G→A | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,761,889 | C→A | D388Y (GAT→TAT) | folC ← | tetrahydrofolate synthase |
| RA | 1,769,572 | A→G | V295V (GTT→GTC) | hemB ← | porphobilinogen synthase |
| RA | 1,830,883 | C→T | K79K (AAG→AAA) | ezrA ← | possible septation ring formation regulator |
| RA | 1,851,260 | C→A | A115S (GCG→TCG) | acsA1 ← | acetate‑‑CoA ligase |
| RA | 1,932,853 | T→C | I799V (ATT→GTT) | USA300HOU_1798 ← | hypothetical protein |
| RA | 1,963,768 | C→G | V365L (GTA→CTA) | hemG ← | protoporphyrinogen oxidase |
| RA | 2,004,062 | (A)8→7 | intergenic (‑649/+99) | rrs3 ← / ← perR | 16S ribosomal RNA/Fur family transcriptional regulator |
| RA | 2,010,363 | C→T | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,018,612 | G→A | R103* (CGA→TGA) | mgt ← | transglycosylase |
| RA | 2,078,573 | (T)7→8 | coding (246/681 nt) | USA300HOU_1935 ← | hypothetical membrane protein |
| RA | 2,079,114 | T→C | H201R (CAC→CGC) | bcrA ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 2,086,905 | (A)8→7 | intergenic (‑56/‑629) | USA300HOU_1946 ← / → chp | hypothetical protein/chemotaxis inhibitory protein CHIPS |
| RA | 2,272,733 | C→T | intergenic (‑321/‑342) | glmS ← / → mtlF | glutamine‑‑fructose‑6‑phosphate transaminase (isomerizing)/PTS family fructose/mannitol (fru) porter component IIBC |
| RA | 2,279,705 | G→A | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,352,815 | G→A | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,454,626 | A→T | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,502,887 | (A)5→6 | coding (1411/2106 nt) | USA300HOU_2364 → | AraC transcriptional regulator |
| RA | 2,532,298 | A→T | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,543,088 | G→A | R283K (AGA→AAA) | hlgA → | gamma‑hemolysin component A |
| RA | 2,679,462 | (A)8→7 | intergenic (+334/‑55) | USA300HOU_2535 → / → cbpD | hypothetical protein/possible secretory antigen |
| RA | 2,709,444 | (T)6→5 | coding (1483/1812 nt) | oatA ← | possible acetyltransferase |
| RA | 2,750,562 | T→C | V197V (GTA→GTG) | betA ← | choline dehydrogenase |
| RA | 2,787,510 | T→C | intergenic (+56/‑184) | USA300HOU_2639 → / → USA300HOU_2640 | hypothetical protein/BglG family transcriptional antiterminator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP000730 | 2176699–2181130 | 2181130 | 1–4432 | 10 [9] | [9] 10 | [rrl4]–[rrs4] | [rrl4],[rrs4] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 40 (1.050) | 31 (1.120) +40 bp |
19/214 | 0.3 | 51.6% | 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 | |||||