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 | 37,746 | A→T | 30.5% | intergenic (+442/‑67) | USA300HOU_0028 → / → ugpQ1 | hypothetical protein/glycerophosphodiester phosphodiesterase |
| RA | 39,246 | C→T | 50.0% | A630T (GCT→ACT) | mecA ← | penicillin binding protein 2 prime |
| RA | 39,378 | C→A | 43.3% | D586Y (GAT→TAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 71,870 | T→C | 8.9% | A368A (GCA→GCG) | arcD1 ← | arginine/ornithine APC family amino acid‑polyamine‑organocation transporter, antiporter |
| RA | 71,990 | A→G | 9.1% | N328N (AAT→AAC) | arcD1 ← | arginine/ornithine APC family amino acid‑polyamine‑organocation transporter, antiporter |
| RA | 110,651 | C→T | 10.6% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 15.0% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 27.4% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 26.1% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 225,710 | C→G | 61.4% | T266R (ACA→AGA) | USA300HOU_0205 → | possible sugar phosphate isomerase |
| RA | 299,913 | T→A | 8.7% | H60Q (CAT→CAA) | USA300HOU_0266 → | 2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase |
| RA | 367,644 | G→T | 100% | intergenic (‑96/‑20) | nanA ← / → USA300HOU_0336 | N‑acetylneuraminate lyase/possible transcriptional regulator |
| RA | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_0458 → | hypothetical protein |
| RA | 512,643 | A→G | 44.7% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 531,823 | A→G | 13.4% | intergenic (+1394/‑4331) | USA300HOU_0494 → / → rplY | hypothetical protein/ribosomal protein L25 |
| RA | 638,614 | G→T | 100% | T14K (ACA→AAA) | thiD ← | phosphomethylpyrimidine kinase |
| RA | 707,879 | A→T | 100% | L11I (TTA→ATA) | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 730,534 | C→T | 18.7% | intergenic (+141/‑188) | USA300HOU_0676 → / → USA300HOU_0677 | possible S9C family peptidase/hypothetical protein |
| RA | 787,110 | C→T | 16.6% | R146C (CGC→TGC) | pabB → | anthranilate synthase |
| RA | 790,778 | G→A | 100% | intergenic (+277/‑197) | USA300HOU_0741 → / → USA300HOU_0742 | possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| RA | 849,263 | C→A | 41.9% | A130E (GCA→GAA) | USA300HOU_0794 → | ATP‑binding protein |
| RA | 880,093 | G→T | 33.3% | intergenic (+271/‑70) | USA300HOU_0822 → / → nuc | hypothetical protein/micrococcal nuclease |
| RA | 1,064,082 | G→T | 19.0% | A136E (GCA→GAA) | USA300HOU_1000 ← | LytR family transcriptional regulator |
| RA | 1,226,031 | G→T | 15.2% | V40L (GTA→TTA) | USA300HOU_1151 → | hypothetical lipoprotein |
| RA | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,233,332 | C→A | 57.9% | P413T (CCT→ACT) | 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 | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA ← | cold shock protein CspA |
| RA | 1,474,639 | C→G | 100% | A9129P (GCA→CCA) | ebh ← | extracellular matrix binding protein |
| RA | 1,481,355 | G→T | 100% | A6890E (GCA→GAA) | ebh ← | extracellular matrix binding protein |
| 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 | 1,650,833 | A→C | 11.6% | S5A (TCA→GCA) | gcvPB ← | glycine dehydrogenase (decarboxylating) subunit 2 |
| RA | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,775,439 | C→T | 62.6% | G362D (GGT→GAT) | clpX ← | S14 family endopeptidase ClpX |
| RA | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | USA300HOU_1679 ← | sensor histidine kinase |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,013,179 | A→T | 30.2% | Q19H (CAA→CAT) | USA300HOU_1864 → | possible metal‑dependent hydrolase |
| RA | 2,028,542 | G→C | 32.7% | L35V (CTC→GTC) | USA300HOU_1882 ← | hypothetical membrane protein |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,367,543 | T→C | 10.5% | intergenic (‑660/+4898) | rpmC ← / ← USA300HOU_2234 | ribosomal protein L29/NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | USA300HOU_2698 → | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 40 (1.330) | 23 (1.100) +40 bp |
20/180 | NT | 45.5% | 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 | = 800928 | 29 (0.960) | 3 (0.110) | 3/246 | NT | 10.1% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 26 (0.910) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||