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 | 8,822 | A→T | 10.6% | E597D (GAA→GAT) | gyrA → | DNA topoisomerase (ATP‑hydrolyzing) subunit A |
| RA | 39,378 | C→A | 100% | D586Y (GAT→TAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 110,660 | T→A | 14.3% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 27.7% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 29.2% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 18.6% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 367,644 | G→T | 100% | intergenic (‑96/‑20) | nanA ← / → USA300HOU_0336 | N‑acetylneuraminate lyase/possible transcriptional regulator |
| RA | 408,719 | T→C | 16.6% | L491L (TTA→TTG) | metE ← | 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase |
| RA | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_0458 → | hypothetical protein |
| RA | 512,643 | A→G | 51.0% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| 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 | 790,778 | G→A | 100% | intergenic (+277/‑197) | USA300HOU_0741 → / → USA300HOU_0742 | possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| RA | 1,064,126 | G→C | 100% | Y121* (TAC→TAG) | USA300HOU_1000 ← | LytR family transcriptional regulator |
| RA | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| RA | 1,238,307 | C→T | 100% | Q141* (CAA→TAA) | USA300HOU_1162 → | glycerone kinase |
| RA | 1,274,212 | A→T | 100% | K205N (AAA→AAT) | USA300HOU_1186 → | CodY family transcriptional regulator |
| RA | 1,318,237 | T→A | 100% | F124Y (TTT→TAT) | miaB → | 2‑methylthioadenine synthetase |
| RA | 1,345,220 | A→G | 18.8% | intergenic (+32/‑18) | USA300HOU_1256 → / → USA300HOU_1257 | hypothetical protein/hypothetical protein |
| 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 | 1,555,359 | A→G | 13.8% | intergenic (+55/+51) | fer → / ← USA300HOU_1423 | ferredoxin/hypothetical membrane protein |
| RA | 1,607,132 | C→T | 100% | intergenic (+1247/+815) | USA300HOU_1490 → / ← USA300HOU_1492 | integrase/possible lipoprotein |
| RA | 1,644,319 | C→T | 8.7% | K72K (AAG→AAA) | accB ← | biotin carboxyl carrier subunit |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,770,911 | T→A | 100% | S73C (AGT→TGT) | hemD ← | uroporphyrinogen‑III synthase |
| RA | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | USA300HOU_1679 ← | sensor histidine kinase |
| RA | 1,805,508 | C→T | 50.0% | G535S (GGT→AGT) | pykA ← | pyruvate kinase |
| RA | 1,883,654 | C→T | 100% | G522D (GGT→GAT) | fmtB1 ← | cell surface anchored protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,018,733:1 | (A)6→7 | 100% | coding (186/810 nt) | USA300HOU_1869 ← | transglycosylase |
| RA | 2,143,110 | G→A | 100% | V163V (GTG→GTA) | USA300HOU_2026 → | hypothetical membrane protein |
| RA | 2,205,303 | G→A | 15.4% | L273F (CTT→TTT) | ddlA ← | D‑alanine‑‑D‑alanine ligase |
| RA | 2,274,965 | G→C | 100% | E106D (GAG→GAC) | bglG → | transcriptional antiterminator |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,315,088 | T→A | 100% | K61I (AAA→ATA) | USA300HOU_2172 ← | MFS family major facilitator transporter |
| RA | 2,342,380 | A→C | 100% | L78V (TTG→GTG) | USA300HOU_2199 ← | possible HAD superfamily hydrolase |
| RA | 2,388,866 | A→G | 100% | G8G (GGA→GGG) | USA300HOU_2249 → | hypothetical protein |
| RA | 2,504,889 | G→A | 13.5% | intergenic (+193/+211) | USA300HOU_2365 → / ← gltT | hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter |
| RA | 2,504,894 | C→T | 18.0% | intergenic (+198/+206) | USA300HOU_2365 → / ← gltT | hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter |
| RA | 2,504,896 | G→C | 16.8% | intergenic (+200/+204) | USA300HOU_2365 → / ← gltT | hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter |
| RA | 2,504,957 | G→C | 11.7% | intergenic (+261/+143) | USA300HOU_2365 → / ← gltT | hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter |
| RA | 2,504,989 | T→C | 10.0% | 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) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,679,650 | G→A | 100% | C45Y (TGT→TAT) | USA300HOU_2536 → | possible secretory antigen |
| RA | 2,709,600 | (T)5→4 | 100% | coding (1327/1812 nt) | USA300HOU_2562 ← | possible acetyltransferase |
| 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 = | 20 (0.800) | 16 (0.990) +45 bp |
13/170 | NT | 45.0% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 2176447 = | 40 (1.610) | noncoding (114/114 nt) | rrf5 | 5S ribosomal RNA | |||||