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 | 39,378 | C→A | 100% | D586Y (GAT→TAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 13.0% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 29.0% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 29.4% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 10.3% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 462,218 | A→T | 11.2% | K329I (AAA→ATA) | USA300HOU_RS02185 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 499,857 | C→T | 16.5% | A854V (GCG→GTG) | gltA → | Glutamate synthase [NADPH] large chain |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 43.9% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 531,519 | G→A | 15.9% | A261T (GCA→ACA) ‡ | ispE → | 4‑diphosphocytidyl‑2‑C‑methyl‑D‑erythritol kinase |
| RA | USA300TCH1516_ALE | 531,520 | C→A | 17.7% | A261E (GCA→GAA) ‡ | ispE → | 4‑diphosphocytidyl‑2‑C‑methyl‑D‑erythritol kinase |
| RA | USA300TCH1516_ALE | 567,389 | A→T | 60.8% | Q98L (CAA→CTA) | ctsR → | Transcriptional regulator CtsR |
| RA | USA300TCH1516_ALE | 587,957 | G→T | 58.6% | A621S (GCG→TCG) | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | USA300TCH1516_ALE | 667,603 | G→A | 8.8% | intergenic (+86/‑413) | USA300TCH1516_00600 → / → adh | hypothetical protein/Alcohol dehydrogenase |
| RA | USA300TCH1516_ALE | 677,166 | T→G | 13.8% | Y15D (TAC→GAC) | USA300HOU_RS03265 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 945,717 | C→T | 6.5% | A776T (GCA→ACA) | mnhA1 ← | Na(+)/H(+) antiporter subunit A1 |
| RA | USA300TCH1516_ALE | 964,580 | T→C | 9.0% | F709L (TTT→CTT) | addB → | ATP‑dependent helicase/deoxyribonuclease subunit B |
| RA | USA300TCH1516_ALE | 982,331 | T→C | 5.5% | D67D (GAT→GAC) | USA300HOU_RS04855 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,000,948 | C→T | 64.3% | T11I (ACA→ATA) | spxA → | Regulatory protein Spx |
| RA | USA300TCH1516_ALE | 1,083,479 | T→C | 6.5% | G33G (GGT→GGC) | purD → | Phosphoribosylamine‑‑glycine ligase |
| RA | USA300TCH1516_ALE | 1,231,396 | G→T | 19.0% | R14I (AGA→ATA) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,231,407 | G→A | 50.8% | E18K (GAA→AAA) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,231,720 | G→A | 12.3% | R122K (AGA→AAA) | stp → | Serine/threonine phosphatase stp |
| 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 | 1,516,802 | A→T | 9.0% | intergenic (‑8/+6) | gpsB ← / ← USA300HOU_RS07400 | Cell cycle protein GpsB/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,693,509 | A→G | 5.5% | L10S (TTA→TCA) | hrcA ← | Heat‑inducible transcription repressor HrcA |
| RA | USA300TCH1516_ALE | 1,716,758 | C→T | 11.3% | E77K (GAA→AAA) | kipI_2 ← | Kinase A inhibitor |
| RA | USA300TCH1516_ALE | 1,744,443 | C→A | 59.3% | V77F (GTT→TTT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,759,201 | T→A | 20.9% | L31F (TTA→TTT) | USA300HOU_RS08780 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,817,305 | G→A | 9.6% | A153V (GCG→GTG) | USA300HOU_RS09040 ← | Cobalt‑dependent inorganic pyrophosphatase |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,227,320 | T→G | 23.9% | I40L (ATT→CTT) | atpB ← | ATP synthase subunit a |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,372,559 | C→T | 5.5% | C406Y (TGT→TAT) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,506 | A→T | 30.0% | N90K (AAT→AAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,436,416 | A→G | 10.2% | L28P (CTT→CCT) | yifK ← | putative transport protein YifK |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,701,061 | C→T | 8.7% | M266I (ATG→ATA) | bacF ← | Transaminase BacF |
| RA | USA300TCH1516_ALE | 2,704,755 | C→T | 12.0% | G360S (GGT→AGT) | crtQ ← | 4,4'‑diaponeurosporenoate glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,774,873 | A→G | 7.5% | D771D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,797,361 | T→C | 6.1% | S503S (TCT→TCC) | USA300HOU_RS14370 → | N‑acetylmuramoyl‑L‑alanine amidase domain‑containing protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | USA300TCH1516_ALE | 2176686–2181131 | 2181131 | 1–4446 | 25 [24] | [24] 25 | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 450716 | 24 (0.370) | 33 (0.590) | 27/226 | NT | 63.6% | intergenic (+83/‑281) | speC_3/tst_2 | Exotoxin type C/Toxic shock syndrome toxin‑1 |
| ? | USA300TCH1516_ALE | 451778 = | 17 (0.300) | intergenic (+77/‑369) | tst_2/USA300HOU_RS02140 | Toxic shock syndrome toxin‑1/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 85 (1.320) | 50 (1.130) +40 bp |
35/180 | NT | 46.0% | 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 (0.920) | 4 (0.070) | 4/226 | NT | 7.8% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 44 (0.790) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 70 (1.090) | 13 (0.230) | 10/232 | NT | 19.8% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 43 (0.750) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||