mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 2,002,507 | 0 | C | T | 75.0% | 355.8 / 120.7 | 176 | noncoding (907/1540 nt) | rrs3 | 16S ribosomal RNA |
| * | CP000730 | 512,643 | 0 | A | G | 73.9% | 113.6 / 44.8 | 65 | intergenic (+711/‑150) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| * | CP000730 | 2,002,497 | 0 | C | A | 67.4% | 257.3 / 206.7 | 184 | noncoding (917/1540 nt) | rrs3 | 16S ribosomal RNA |
| * | CP000730 | 2,002,484 | 0 | T | C | 60.5% | 187.6 / 217.0 | 185 | noncoding (930/1540 nt) | rrs3 | 16S ribosomal RNA |
| * | CP000730 | 602,466 | 0 | G | T | 43.8% | 7.7 / 10.0 | 16 | intergenic (+56/‑101) | hchA/araB | possible hydrolase/ribulokinase |
| * | CP000730 | 2,002,448 | 0 | T | A | 35.7% | 108.5 / 229.1 | 199 | noncoding (966/1540 nt) | rrs3 | 16S ribosomal RNA |
| * | CP000730 | 129,708 | 1 | . | T | 30.8% | 18.3 / 12.4 | 13 | intergenic (‑85/+300) | spa/sarH1 | immunoglobulin G binding protein A/staphylococcal accessory regulator H1 |
| * | CP000730 | 2,124,528 | 0 | A | G | 28.6% | 79.7 / 16.2 | 42 | D219G (GAC→GGC) | USA300HOU_2004 | possible bifunctional S24 family peptidase/transcriptional regulator |
| * | CP000730 | 2,124,513 | 0 | T | G | 22.7% | 97.2 / 11.2 | 44 | L214R (CTA→CGA) | USA300HOU_2004 | possible bifunctional S24 family peptidase/transcriptional regulator |
| * | CP000730 | 2,124,517 | 0 | T | C | 22.7% | 105.0 / 11.2 | 44 | N215N (AAT→AAC) | USA300HOU_2004 | possible bifunctional S24 family peptidase/transcriptional regulator |
| * | CP000730 | 2,290,749 | 0 | A | G | 22.2% | 56.6 / 17.5 | 36 | intergenic (‑163/‑63) | arg/USA300HOU_2155 | arginase/transposase |
| * | CP000730 | 2,558,636 | 0 | A | T | 22.2% | 104.1 / 10.1 | 45 | L14F (TTA→TTT) | bcr | MFS family major facilitator transporter, bicyclomycin:cation symporter |
| * | CP000730 | 2,124,527 | 0 | G | C | 21.4% | 107.4 / 14.7 | 42 | D219H (GAC→CAC) | USA300HOU_2004 | possible bifunctional S24 family peptidase/transcriptional regulator |
| * | CP000730 | 2,124,523 | 0 | T | C | 20.4% | 97.1 / 11.7 | 44 | D217D (GAT→GAC) | USA300HOU_2004 | possible bifunctional S24 family peptidase/transcriptional regulator |
| Marginal new junction evidence (lowest skew 10 of 29 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 2687481 | 83 (1.200) | 5 (0.080) | 5/278 | 1.9 | 6.0% | intergenic (+35/+34) | clp/USA300HOU_2543 | S14 family endopeptidase Clp/hypothetical protein |
| ? | CP000730 | = 2687499 | 81 (1.270) | intergenic (+53/+16) | clp/USA300HOU_2543 | S14 family endopeptidase Clp/hypothetical protein | |||||
| * | ? | CP000730 | = 588673 | 134 (1.940) | 5 (0.080) | 5/284 | 1.9 | 3.7% | coding (2577/3552 nt) | rpoB | DNA‑directed RNA polymerase subunit beta |
| ? | CP000730 | = 588680 | 130 (1.990) | coding (2584/3552 nt) | rpoB | DNA‑directed RNA polymerase subunit beta | |||||
| * | ? | CP000730 | 705321 = | 74 (1.070) | 4 (0.060) | 4/282 | 2.1 | 5.5% | intergenic (+1071/+89) | nhaK/psaA | possible CPA1 family monovalent cation (K+ or Na+):proton (H+) antiporter‑1/ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | 705378 = | 67 (1.030) | intergenic (+1128/+32) | nhaK/psaA | possible CPA1 family monovalent cation (K+ or Na+):proton (H+) antiporter‑1/ABC superfamily ATP binding cassette transporter, binding protein | |||||
| * | ? | CP000730 | 338068 = | 110 (1.590) | 4 (0.060) | 4/282 | 2.1 | 4.0% | coding (2206/4440 nt) | essC | virulence protein EssC |
| ? | CP000730 | 338130 = | 90 (1.390) | coding (2268/4440 nt) | essC | virulence protein EssC | |||||
| * | ? | CP000730 | 82395 = | 137 (1.980) | 8 (0.120) | 4/292 | 2.1 | 5.7% | coding (500/957 nt) | nikA | nickel (Ni2+)/peptide ABC superfamily ATP binding cassette transporter, membrane protein |
| ? | CP000730 | 82432 = | 132 (1.960) | coding (537/957 nt) | nikA | nickel (Ni2+)/peptide ABC superfamily ATP binding cassette transporter, membrane protein | |||||
| * | ? | CP000730 | 2812209 = | 252 (3.650) | 3 (0.050) | 3/280 | 2.2 | 1.3% | coding (6120/6816 nt) | sasA | serine‑threonine rich protein |
| ? | CP000730 | 2812258 = | 213 (3.310) | coding (6071/6816 nt) | sasA | serine‑threonine rich protein | |||||
| * | ? | CP000730 | = 2460586 | 89 (1.290) | 3 (0.050) | 3/278 | 2.2 | 3.5% | coding (689/900 nt) | natA | ABC superfamily ATP binding cassette transporter, ABC protein |
| ? | CP000730 | = 2460640 | 85 (1.330) | coding (635/900 nt) | natA | ABC superfamily ATP binding cassette transporter, ABC protein | |||||
| * | ? | CP000730 | 1441573 = | 50 (0.720) | 4 (0.060) | 3/282 | 2.2 | 8.0% | coding (598/624 nt) | xpaC | 5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC |
| ? | CP000730 | 1441605 = | 45 (0.690) | intergenic (+6/‑26) | xpaC/telA | 5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC/tellurite resistance protein | |||||
| * | ? | CP000730 | 1409145 = | 109 (1.580) | 3 (0.050) | 3/278 | 2.2 | 2.9% | coding (410/1215 nt) | trpB | tryptophan synthase beta subunit |
| ? | CP000730 | 1409186 = | 103 (1.610) | coding (451/1215 nt) | trpB | tryptophan synthase beta subunit | |||||
| * | ? | CP000730 | 1236098 = | 70 (1.010) | 3 (0.050) | 3/282 | 2.2 | 4.9% | coding (254/642 nt) | yloS | thiamine diphosphokinase |
| ? | CP000730 | 1236143 = | 50 (0.770) | coding (299/642 nt) | yloS | thiamine diphosphokinase | |||||