mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 66,465 | T→C | 5.6% | R14R (AGA→AGG) | USA300HOU_0062 ← | hypothetical protein |
| RA | 76,969 | G→A | 100% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 94,785 | A→G | 6.9% | T212T (ACA→ACG) | USA300HOU_0093 → | hypothetical protein |
| RA | 96,144 | A→G | 8.6% | intergenic (+660/+819) | USA300HOU_0093 → / ← USA300HOU_0095 | hypothetical protein/hypothetical protein |
| RA | 110,651 | C→T | 10.5% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 13.0% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 42.8% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 40.0% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 9.9% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 195,286 | T→A | 100% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 312,003 | A→G | 5.8% | K165E (AAA→GAA) | bglA → | 6‑phospho‑beta‑glucosidase |
| RA | 396,540 | G→A | 100% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 426,904 | T→A | 4.3% | E140V (GAA→GTA) | USA300HOU_0401 ← | hypothetical protein |
| RA | 456,707 | T→A | 6.1% | S88R (AGT→AGA) | set25 → | staphylococcal exotoxin |
| RA | 512,643 | A→G | 52.6% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 607,884 | G→A | 100% | R209* (CGA→TGA) | USA300HOU_0550 ← | deoxynucleoside kinase |
| RA | 629,681 | C→A | 100% | L84I (CTA→ATA) | USA300HOU_0564 → | possible 3‑hexulose‑6‑phosphate synthase |
| RA | 637,932 | G→A | 5.1% | V241V (GTC→GTT) | thiD ← | phosphomethylpyrimidine kinase |
| RA | 665,392 | T→G | 100% | L79* (TTA→TGA) | USA300HOU_0608 → | possible acetytransferase |
| RA | 667,735 | A→C | 5.4% | intergenic (+767/‑281) | USA300HOU_0609 → / → adh | phosphohydrolase/alcohol dehydrogenase |
| RA | 707,910 | A→G | 100% | intergenic (‑1/‑121) | USA300HOU_0653 ← / → USA300HOU_0654 | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 712,088 | T→C | 7.9% | L134S (TTA→TCA) | tagG → | teichoic acid ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 835,012 | G→T | 6.9% | M229I (ATG→ATT) | prfB → | peptide chain release factor 2 |
| RA | 903,873 | A→G | 6.3% | intergenic (+148/‑523) | USA300HOU_0861 → / → USA300HOU_0862 | possible DNA primase/hypothetical protein |
| RA | 1,210,010 | G→C | 4.8% | E146Q (GAA→CAA) | pyrB → | aspartate carbamoyltransferase |
| RA | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,435,069 | A→C | 23.2% | T142T (ACA→ACC) | dapD → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑succinyltransferase |
| RA | 1,438,346 | C→T | 6.2% | Q204* (CAG→TAG) | lysA2 → | diaminopimelate decarboxylase |
| RA | 1,440,085 | G→T | 100% | intergenic (‑45/‑891) | cspA ← / → xpaC | cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC |
| RA | 1,507,565 | G→A | 6.3% | A4V (GCA→GTA) | ald1 ← | alanine dehydrogenase |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,677,731 | A→G | 5.5% | E290G (GAG→GGG) | glyS → | glycine‑‑tRNA ligase |
| RA | 1,744,362 | G→A | 100% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,761,889 | C→A | 100% | D388Y (GAT→TAT) | folC ← | tetrahydrofolate synthase |
| RA | 1,783,940 | T→C | 6.6% | M381V (ATG→GTG) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,794,352 | A→T | 5.4% | Y431N (TAT→AAT) | USA300HOU_1678 ← | hypothetical membrane protein |
| RA | 1,857,700 | A→G | 7.3% | I225T (ATA→ACA) | USA300HOU_1728 ← | hypothetical protein |
| RA | 1,874,676 | T→C | 5.4% | E178G (GAA→GGA) | rsuA ← | pseudouridylate synthase |
| RA | 1,963,768 | C→G | 100% | 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 | 2,018,834 | G→C | 11.2% | P29A (CCA→GCA) | USA300HOU_1869 ← | transglycosylase |
| RA | 2,026,958 | C→T | 5.2% | G330D (GGT→GAT) | vraS ← | sensor histidine kinase VraS |
| RA | 2,186,126 | G→T | 7.1% | S12* (TCA→TAA) | fliA ← | DNA‑directed RNA polymerase sigma subunit FliA |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,352,815 | G→A | 100% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,399,409 | C→G | 4.8% | E154Q (GAA→CAA) | USA300HOU_2263 ← | acetyltransferase |
| RA | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,458,481 | T→C | 6.5% | R32R (AGA→AGG) | USA300HOU_2319 ← | aldose 1‑epimerase |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,707,179 | A→G | 5.3% | F51F (TTT→TTC) | USA300HOU_2559 ← | phytoene dehydrogenase |
| RA | 2,775,053 | A→G | 6.6% | D711D (GAT→GAC) | clfB ← | clumping factor B |
| RA | 2,857,614 | T→G | 5.5% | intergenic (+10/+55) | USA300HOU_2699 → / ← USA300HOU_2700 | NiCoT family nickel (Ni2+)‑cobalt (Co2+) transporter/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 60 (0.860) | 47 (1.040) +45 bp |
28/170 | NT | 55.0% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 2176447 = | 58 (0.830) | noncoding (114/114 nt) | rrf5 | 5S ribosomal RNA | |||||
| * | ? | CP000730 | 514600 = | NA (NA) | 3 (0.050) | 3/246 | NT | NA | intergenic (+268/‑106) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA |
| ? | CP000730 | 514618 = | NA (NA) | intergenic (+286/‑88) | rrs1/rrl1 | 16S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | CP000730 | 2085296 = | 64 (0.920) | 31 (0.500) | 24/232 | NT | 36.5% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 51 (0.820) | intergenic (+57/+1062) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||