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 299 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 579,146 | 0 | A | G | 79.8% | 592.3 / 154.5 | 264 | intergenic (‑253/+38) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 581,227 | 0 | A | C | 79.4% | 258.4 / 64.9 | 136 | I132L (ATC→CTC) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 580,119 | 0 | A | G | 78.8% | 491.2 / 136.8 | 232 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,120 | 0 | C | T | 78.8% | 549.9 / 125.2 | 233 | intergenic (+34/+131) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 580,115 | 0 | C | T | 78.2% | 554.7 / 123.4 | 234 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 579,385 | 0 | A | G | 78.0% | 747.4 / 231.1 | 363 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,285 | 0 | T | C | 77.8% | 598.7 / 202.8 | 309 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,271 | 0 | G | A | 77.4% | 652.8 / 187.8 | 302 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,540 | 0 | T | C | 77.2% | 804.4 / 275.5 | 401 | N19D (AAC→GAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 581,056 | 0 | A | G | 77.1% | 131.7 / 97.7 | 157 | T75A (ACA→GCA) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 579,457 | 0 | A | G | 76.8% | 697.1 / 244.5 | 358 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,809 | 0 | T | C | 76.8% | 509.0 / 169.7 | 254 | T29A (ACA→GCA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,811 | 0 | T | G | 76.8% | 558.7 / 146.5 | 254 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,671 | 0 | T | C | 76.8% | 643.4 / 229.4 | 341 | intergenic (‑77/‑209) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,502 | 0 | A | G | 76.7% | 797.0 / 285.2 | 416 | N31N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 581,073 | 0 | G | A | 76.5% | 112.6 / 88.7 | 149 | G80G (GGG→GGA) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 581,042 | 0 | T | G | 76.4% | 128.5 / 112.8 | 165 | L70R (CTG→CGG) | nohD | putative DNA‑packaging protein NohD |
| * | NC_000913 | 579,651 | 0 | C | T | 76.3% | 812.5 / 251.8 | 375 | intergenic (‑57/‑229) | ybcV/ybcW | DUF1398 domain‑containing protein YbcV/uncharacterized protein YbcW |
| * | NC_000913 | 579,099 | 0 | A | . | 76.2% | 647.1 / inf | 256 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 580,020 | 0 | G | A | 76.2% | 540.9 / 165.8 | 257 | R47R (AGG→AGA) | ybcW | uncharacterized protein YbcW |
| Marginal new junction evidence (lowest skew 10 of 54 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 270541 = | NA (NA) | 48 (0.440) | 40/596 | 1.7 | 18.5% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 738757 | 211 (1.950) | coding (666/762 nt) | ybfD | H repeat‑associated putative transposase YbfD | |||||
| * | ? | NC_000913 | 738756 = | 213 (1.980) | 46 (0.430) | 36/592 | 2.1 | 17.8% | coding (665/762 nt) | ybfD | H repeat‑associated putative transposase YbfD |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 689045 | NA (NA) | 49 (0.450) | 33/598 | 2.5 | 19.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 716576 = | 206 (1.900) | intergenic (+670/+370) | ybfP/potE | lipoprotein YbfP/putrescine transporter PotE | |||||
| * | ? | NC_000913 | = 1907358 | 83 (0.770) | 33 (0.300) | 28/598 | 3.1 | 28.4% | coding (78/210 nt) | cspC | transcription antiterminator and regulator of mRNA stability CspC |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 51 (0.470) | 27/598 | 3.3 | 49.0% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4123908 = | 53 (0.490) | coding (549/1026 nt) | cytR | DNA‑binding transcriptional repressor CytR | |||||
| * | ? | NC_000913 | 3534369 = | 57 (0.530) | 35 (0.320) | 27/598 | 3.3 | 38.0% | coding (1552/1623 nt) | pck | phosphoenolpyruvate carboxykinase (ATP) |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 316483 | NA (NA) | 33 (0.300) | 27/598 | 3.3 | 27.7% | noncoding (1255/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 572469 = | 86 (0.790) | coding (102/102 nt) coding (4/456 nt) |
ylcH ybcN |
uncharacterized protein YlcH DNA base‑flipping protein |
|||||
| * | ? | NC_000913 | 891857 = | 84 (0.770) | 35 (0.320) | 26/598 | 3.4 | 29.4% | coding (674/723 nt) | nfsA | NADPH‑dependent nitro/quinone reductase NfsA |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 2406541 = | 20 (0.180) | 32 (0.300) | 25/582 | 3.5 | 62.5% | coding (101/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA |
| ? | NC_000913 | = 2406549 | 19 (0.180) | coding (93/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA | |||||
| * | ? | NC_000913 | = 780629 | 150 (1.380) | 15 (0.190) | 13/446 | 4.7 | 13.8% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 75 (0.930) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||