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 |
| Marginal read alignment evidence (highest frequency 20 of 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 50.8% | 43.3 / 183.9 | 132 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 45.5% | 25.2 / 97.0 | 77 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 41.2% | 83.1 / 110.4 | 102 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 40.2% | 76.0 / 103.0 | 97 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,089 | 0 | G | C | 32.0% | 30.7 / 14.4 | 26 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,751,081 | 0 | C | A | 31.0% | 38.7 / 15.5 | 29 | S147* (TCG→TAG) | PP_1551 | replication protein O |
| * | NC_002947 | 2,282,770 | 0 | T | G | 30.7% | 65.6 / 74.8 | 89 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,340,076 | 0 | G | C | 30.4% | 25.2 / 14.3 | 23 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,282,779 | 0 | C | A | 28.9% | 106.4 / 53.4 | 83 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 195,559 | 0 | C | A | 28.6% | 137.7 / 51.7 | 77 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,075 | 0 | A | T | 28.0% | 26.9 / 12.7 | 26 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,282,775 | 0 | G | C | 27.4% | 123.3 / 55.3 | 84 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,340,083 | 0 | A | G | 27.3% | 27.2 / 10.8 | 22 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 197,590 | 0 | T | C | 27.0% | 187.5 / 77.2 | 116 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,494 | 0 | C | G | 26.7% | 47.9 / 15.6 | 30 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 5,905,075 | 0 | A | T | 26.5% | 102.1 / 44.8 | 68 | L196Q (CTG→CAG) | spuG | spermidine/putrescine ABC transporter permease |
| * | NC_002947 | 1,013,248 | 0 | A | T | 26.2% | 72.2 / 20.6 | 42 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 2,282,774 | 0 | G | C | 26.2% | 117.9 / 58.3 | 84 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 196,351 | 0 | C | G | 25.6% | 137.2 / 52.5 | 79 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,489 | 0 | C | A | 25.0% | 45.4 / 13.4 | 28 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| Marginal new junction evidence (lowest skew 10 of 442 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808174 = | 5 (0.070) | 16 (0.320) | 13/210 | 4.0 | 44.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988935 | 37 (0.740) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652782 | 52 (0.780) | 16 (0.280) | 15/240 | 4.2 | 41.2% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 1 (0.020) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808179 | 5 (0.070) | 24 (0.390) | 13/256 | 5.1 | 39.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 70 (1.150) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 1499507 = | 36 (0.540) | 16 (0.260) | 13/256 | 5.1 | 23.9% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947 | = 6060505 | 69 (1.130) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947 | 2050559 = | 39 (0.580) | 8 (0.160) | 8/206 | 5.6 | 25.9% | intergenic (‑52/+123) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947 | 2050669 = | 17 (0.350) | intergenic (‑162/+13) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 5914184 | 42 (0.630) | 10 (0.190) | 9/224 | 5.7 | 22.1% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | = 5914224 | 37 (0.690) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | = 5453138 | 4 (0.060) | 8 (0.180) +48 bp |
6/184 | 5.9 | 36.1% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5545626 = | 39 (0.580) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5224500 = | 13 (0.190) | 8 (0.180) +48 bp |
6/184 | 5.9 | 31.9% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947 | 5545626 = | 39 (0.580) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5222887 = | NA (NA) | 7 (0.160) +48 bp |
6/184 | 5.9 | 72.7% | intergenic (‑298/+81) | PP_4602/PP_4603 | AraC family transcriptional regulator/transposase |
| ? | NC_002947 | = 5453138 | 4 (0.060) | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase | |||||
| * | ? | NC_002947 | 5222887 = | NA (NA) | 7 (0.160) +48 bp |
6/184 | 5.9 | 45.0% | intergenic (‑298/+81) | PP_4602/PP_4603 | AraC family transcriptional regulator/transposase |
| ? | NC_002947 | 5224500 = | 13 (0.190) | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease | |||||