mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
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 | ||
| * | NC_000913 | 4,392,506 | 0 | C | G | 29.4% | 17.4 / 11.7 | 18 | noncoding (35/76 nt) | glyX | tRNA‑Gly |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.6% | 68.7 / 29.0 | 42 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,330,402 | 0 | A | . | 24.2% | 83.5 / 24.3 | 34 | intergenic (+21/+15) | sohB/yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN |
| * | NC_000913 | 1,330,399 | 0 | A | T | 23.5% | 62.2 / 18.0 | 34 | intergenic (+18/+18) | sohB/yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN |
| * | NC_000913 | 1,795,228 | 0 | G | C | 23.5% | 68.7 / 22.4 | 36 | intergenic (‑76/+25) | btuC/ihfA | vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit |
| * | NC_000913 | 654,560 | 0 | A | C | 23.1% | 42.4 / 14.8 | 26 | intergenic (+18/+23) | citB/dcuC | response regulator in two‑component regulatory system with CitA/anaerobic C4‑dicarboxylate transport |
| * | NC_000913 | 1,330,396 | 1 | . | T | 22.2% | 83.3 / 32.9 | 36 | intergenic (+15/+21) | sohB/yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN |
| * | NC_000913 | 1,795,227 | 0 | A | T | 22.2% | 70.9 / 11.2 | 36 | intergenic (‑75/+26) | btuC/ihfA | vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit |
| * | NC_000913 | 1,795,229 | 0 | A | T | 22.2% | 56.7 / 16.1 | 36 | intergenic (‑77/+24) | btuC/ihfA | vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit |
| * | NC_000913 | 2,462,881 | 0 | C | . | 22.2% | 34.9 / 10.1 | 18 | intergenic (+235/‑131) | fadL/yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| * | NC_000913 | 1,620,224 | 0 | C | G | 20.8% | 49.5 / 10.0 | 24 | intergenic (+17/+14) | marB/eamA | periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system |
| * | NC_000913 | 1,620,227 | 0 | C | G | 20.8% | 52.9 / 10.9 | 24 | intergenic (+20/+11) | marB/eamA | periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system |
| * | NC_000913 | 2,521,344 | 0 | C | T | 20.0% | 97.3 / 17.5 | 45 | intergenic (+16/+249) | lysV/xapR | tRNA‑Lys/transcriptional activator of xapAB |
| Marginal new junction evidence (lowest skew 10 of 59 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1570598 = | 49 (1.240) | 6 (0.170) +CCGTTACCGTTAAAC |
6/232 | 3.6 | 13.1% | intergenic (‑109/+47) | gadC/gadB | glutamate:gamma‑aminobutyric acid antiporter/glutamate decarboxylase B, PLP‑dependent |
| ? | NC_000913 | 3666176 = | 41 (1.040) | intergenic (‑366/+4) | gadX/gadA | acid resistance regulon transcriptional activator; autoactivator/glutamate decarboxylase A, PLP‑dependent | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.680) | 7 (0.200) | 6/230 | 3.6 | 21.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 27 (0.780) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 4474083 = | 61 (1.550) | 6 (0.170) | 6/240 | 3.7 | 10.0% | intergenic (‑30/‑41) | bdcA/bdcR | c‑di‑GMP‑binding biofilm dispersal mediator protein/transcriptional repressor for divergent bdcA |
| ? | NC_000913 | 4474127 = | 52 (1.440) | coding (4/594 nt) | bdcR | transcriptional repressor for divergent bdcA | |||||
| * | ? | NC_000913 | = 2539674 | NA (NA) | 7 (0.190) | 6/248 | 3.8 | NA | intergenic (‑91/+43) | cysM/cysA | cysteine synthase B (O‑acetylserine sulfhydrolase B)/sulfate/thiosulfate transporter subunit |
| ? | NC_000913 | = 2539688 | NA (NA) | intergenic (‑105/+29) | cysM/cysA | cysteine synthase B (O‑acetylserine sulfhydrolase B)/sulfate/thiosulfate transporter subunit | |||||
| * | ? | NC_000913 | = 2305015 | 30 (0.760) | 5 (0.170) +33 bp |
4/196 | 3.8 | 18.3% | noncoding (599/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 2305065 | NA (NA) | noncoding (649/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | 1784702 = | 48 (1.220) | 5 (0.130) | 5/246 | 4.2 | 9.9% | intergenic (+25/+32) | fadK/ppsA | short chain acyl‑CoA synthetase, anaerobic/phosphoenolpyruvate synthase |
| ? | NC_000913 | 1784727 = | 46 (1.240) | intergenic (+50/+7) | fadK/ppsA | short chain acyl‑CoA synthetase, anaerobic/phosphoenolpyruvate synthase | |||||
| * | ? | NC_000913 | = 1428264 | NA (NA) | 18 (0.480) | 5/250 | 4.2 | 95.0% | noncoding (531/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2066866 | 1 (0.030) | noncoding (488/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 18 (0.480) | 5/250 | 4.2 | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4502147 = | 32 (0.810) | 4 (0.110) | 4/248 | 4.6 | 13.1% | noncoding (1369/1426 nt) | IS4 | repeat region |
| ? | NC_000913 | 4502181 = | 23 (0.620) | noncoding (1335/1426 nt) | IS4 | repeat region | |||||
| * | ? | NC_000913 | = 4440801 | 39 (0.990) | 4 (0.110) | 4/246 | 4.6 | 10.7% | coding (415/1344 nt) | ytfL | UPF0053 family inner membrane protein |
| ? | NC_000913 | = 4440841 | 30 (0.810) | coding (375/1344 nt) | ytfL | UPF0053 family inner membrane protein | |||||