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 | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000731 | 81 | N→G | 100% | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | 100% | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 12.9% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 18.6% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 30.4% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 30.9% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 10.0% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 460,262 | G→A | 5.8% | intergenic (+111/‑272) | USA300HOU_RS02175 → / → speA_1 | hypothetical protein/Exotoxin type A |
| RA | USA300TCH1516_ALE | 491,927 | T→A | 9.9% | L118L (CTT→CTA) | sle1_1 → | N‑acetylmuramoyl‑L‑alanine amidase sle1 |
| RA | USA300TCH1516_ALE | 494,244 | G→T | 8.2% | R253R (CGC→CGA) | USA300HOU_RS02360 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 44.6% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 620,399 | T→A | 9.0% | V321D (GTC→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 656,852 | T→C | 5.9% | T31T (ACT→ACC) | USA300HOU_RS03140 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 785,677 | G→T | 7.3% | A27E (GCA→GAA) | queC ← | 7‑cyano‑7‑deazaguanine synthase |
| RA | USA300TCH1516_ALE | 1,029,311 | G→A | 5.6% | D707N (GAC→AAC) | USA300HOU_RS05065 → | Serine protease HtrA‑like protein |
| RA | USA300TCH1516_ALE | 1,323,313 | A→G | 6.3% | K29E (AAA→GAA) | mutL → | DNA mismatch repair protein MutL |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,580,165 | G→T | 7.4% | S108* (TCA→TAA) | USA300HOU_RS07740 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,653,690 | G→T | 10.7% | Q97K (CAA→AAA) | aroK ← | Shikimate kinase |
| RA | USA300TCH1516_ALE | 1,684,834 | G→T | 7.3% | S52Y (TCT→TAT) | USA300HOU_RS08395 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,689,325 | T→C | 5.7% | T181A (ACA→GCA) | dnaJ ← | Chaperone protein DnaJ |
| RA | USA300TCH1516_ALE | 1,697,768 | G→A | 6.6% | intergenic (+24/+21) | rpsT → / ← USA300HOU_RS08460 | 30S ribosomal protein S20/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,708,278 | A→G | 7.1% | intergenic (‑306/‑8) | mtnN ← / → USA300HOU_RS08530 | 5'‑methylthioadenosine/S‑adenosylhomocysteine nucleosidase/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,742,872 | A→G | 5.0% | V292A (GTG→GCG) | relA ← | GTP pyrophosphokinase |
| RA | USA300TCH1516_ALE | 1,744,424 | A→G | 11.2% | L83S (TTA→TCA) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,544 | T→C | 58.1% | Y43C (TAC→TGC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,884,975 | T→A | 5.9% | N82Y (AAT→TAT) | ebh_2 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,899,742 | A→G | 11.3% | N421N (AAT→AAC) | USA300HOU_RS09405 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,926,533 | A→G | 5.6% | K114E (AAA→GAA) | USA300HOU_RS09555 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,113,299 | G→T | 6.6% | D38E (GAC→GAA) | USA300HOU_RS10725 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,113,304 | G→T | 7.4% | H37N (CAT→AAT) | USA300HOU_RS10725 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,113,305 | G→T | 7.3% | D36E (GAC→GAA) | USA300HOU_RS10725 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,359,473 | G→T | 7.1% | Q100K (CAA→AAA) | rpsM ← | 30S ribosomal protein S13 |
| RA | USA300TCH1516_ALE | 2,373,506 | A→T | 7.7% | N90K (AAT→AAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,420,667 | G→T | 9.6% | intergenic (+98/‑264) | ssaA2_3 → / → USA300HOU_RS12475 | Staphylococcal secretory antigen ssaA2/Putative 2‑hydroxyacid dehydrogenase |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,575,960 | C→T | 6.2% | V33I (GTT→ATT) | opuCB ← | Carnitine transport permease protein OpuCB |
| RA | USA300TCH1516_ALE | 2,658,932 | G→A | 5.1% | A122V (GCA→GTA) | USA300HOU_RS13680 ← | Putative NAD(P)H nitroreductase |
| RA | USA300TCH1516_ALE | 2,827,998 | T→C | 5.1% | S14P (TCA→CCA) | icaD → | Poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthesis protein IcaD |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 112 (1.230) | 67 (1.070) +40 bp |
36/180 | NT | 46.4% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||
| * | ? | USA300TCH1516_ALE | 895785 = | 59 (0.650) | 27 (0.340) | 15/226 | NT | 33.1% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 58 (0.740) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | 1697752 = | 74 (0.820) | 5 (0.060) | 5/228 | NT | 7.9% | intergenic (+8/+37) | rpsT/USA300HOU_RS08460 | 30S ribosomal protein S20/hypothetical protein |
| ? | USA300TCH1516_ALE | 1697788 = | 51 (0.640) | intergenic (+44/+1) | rpsT/USA300HOU_RS08460 | 30S ribosomal protein S20/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 60 (0.660) | 63 (0.780) | 48/232 | NT | 48.6% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 80 (0.990) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||