mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 123 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 367,573 | 0 | G | A | 55.7% | 62.3 / 188.0 | 141 | intergenic (‑63/+14) | lacI/mhpR | DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional activator MhpR |
| * | NC_000913 | 4,037,496 | 0 | A | T | 49.2% | 79.4 / inf | 189 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 581,335 | 0 | C | A | 44.9% | 51.5 / 160.2 | 127 | L168M (CTG→ATG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,337 | 0 | G | A | 44.9% | 24.7 / 184.4 | 127 | L168L (CTG→CTA) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,322 | 0 | C | T | 44.5% | 15.7 / 167.8 | 119 | A163A (GCC→GCT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,380 | 0 | C | G | 43.0% | 75.9 / 186.1 | 128 | intergenic (+1/‑154) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,381 | 0 | A | G | 43.0% | 64.2 / 167.9 | 128 | intergenic (+2/‑153) | nohD/tfaD | putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD |
| * | NC_000913 | 581,275 | 0 | G | A | 40.2% | 48.9 / 133.0 | 107 | V148I (GTT→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 3,911,533 | 0 | C | A | 39.6% | 166.9 / 22.9 | 111 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 581,289 | 0 | A | G | 39.1% | 94.2 / 110.0 | 110 | K152K (AAA→AAG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,295 | 0 | T | C | 39.1% | 69.4 / 129.9 | 110 | D154D (GAT→GAC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,301 | 0 | C | T | 38.9% | 73.9 / 123.5 | 108 | I156I (ATC→ATT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,291 | 0 | G | A | 38.5% | 74.0 / 110.0 | 111 | R153Q (CGG→CAG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,250 | 0 | T | C | 37.9% | 61.6 / 111.5 | 95 | R139R (CGT→CGC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,253 | 0 | T | C | 37.9% | 86.5 / 89.8 | 95 | F140F (TTT→TTC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 58,065 | 0 | C | A | 37.9% | 143.4 / 18.6 | 103 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 581,241 | 0 | G | T | 37.8% | 84.0 / 100.8 | 98 | V136V (GTG→GTT) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,290 | 0 | C | A | 37.6% | 94.9 / 111.4 | 111 | R153R (CGG→AGG) ‡ | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,259 | 0 | A | G | 37.5% | 65.7 / 108.3 | 97 | E142E (GAA→GAG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,286 | 0 | G | C | 37.1% | 83.9 / 121.3 | 110 | L151L (CTG→CTC) | nohD | putative DNA‑packaging protein NohD |
| Marginal new junction evidence (lowest skew 10 of 130 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3978531 | 25 (0.250) | 36 (0.350) | 23/586 | 3.2 | 59.0% | coding (1007/1080 nt) | wecF | TDP‑N‑acetylfucosamine:lipid II N‑acetylfucosaminyltransferase |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 971729 | 117 (1.140) | 34 (0.330) | 23/590 | 3.3 | 22.5% | intergenic (+131/‑23) | kdsB/ycbJ | 3‑deoxy‑manno‑octulosonate cytidylyltransferase/putative phosphotransferase YcbJ |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 25 (0.240) | 21/590 | 3.6 | 23.6% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 2590459 | 81 (0.790) | coding (2865/3114 nt) | acrD | multidrug efflux pump RND permease AcrD | |||||
| * | ? | NC_000913 | 1390230 = | 52 (0.510) | 25 (0.240) | 21/590 | 3.6 | 32.5% | coding (369/729 nt) | mpaA | murein tripeptide amidase A |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 538183 | 91 (0.890) | 29 (0.280) | 21/586 | 3.6 | 24.2% | coding (551/1455 nt) | ybbW | putative allantoin transporter |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 3536951 = | 89 (0.870) | 30 (0.290) | 20/590 | 3.8 | 25.2% | coding (140/477 nt) | greB | transcription elongation factor GreB |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 25 (0.240) | 20/590 | 3.8 | 16.6% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 4000481 = | 126 (1.230) | coding (576/765 nt) | yigE | DUF2233 domain‑containing protein YigE | |||||
| * | ? | NC_000913 | 971728 = | 120 (1.180) | 27 (0.260) | 20/586 | 3.8 | 18.4% | intergenic (+130/‑24) | kdsB/ycbJ | 3‑deoxy‑manno‑octulosonate cytidylyltransferase/putative phosphotransferase YcbJ |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 4000482 | 129 (1.260) | 33 (0.320) | 19/588 | 4.0 | 20.4% | coding (575/765 nt) | yigE | DUF2233 domain‑containing protein YigE |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 24 (0.230) | 19/590 | 4.0 | 8.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 362930 | 271 (2.640) | coding (250/1254 nt) | lacY | lactose permease | |||||