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 (highest frequency 20 of 117 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,602,010 | 2 | . | C | 74.1% | 63.9 / 21.1 | 27 | coding (193/2019 nt) | hyfB | hydrogenase 4 component B |
| * | NC_000913 | 1,097,219 | 0 | A | G | 63.2% | ‑2.9 / 14.8 | 20 | intergenic (+390/+346) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,097,109 | 0 | A | T | 56.2% | ‑3.1 / 10.4 | 17 | intergenic (+280/+456) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 707,976 | 0 | T | G | 54.5% | ‑1.6 / 24.7 | 33 | intergenic (+219/‑358) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 497,585 | 0 | C | A | 51.8% | 5.7 / 19.4 | 28 | F137L (TTC→TTA) | adk | adenylate kinase |
| * | NC_000913 | 454,906 | 0 | G | T | 50.0% | 14.5 / 13.7 | 49 | intergenic (+117/‑227) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 454,926 | 0 | G | C | 50.0% | 18.8 / 17.2 | 46 | intergenic (+137/‑207) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 2,177,245 | 0 | G | T | 50.0% | ‑0.1 / 28.5 | 54 | intergenic (‑41/+267) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 2,470,427 | 0 | C | A | 50.0% | 38.8 / 12.3 | 47 | Q433K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 3,455,671 | 0 | A | T | 50.0% | 12.3 / 26.0 | 44 | I32F (ATT→TTT) | gspC | Type II secretion system protein GspC |
| * | NC_000913 | 3,455,680 | 0 | G | T | 48.8% | 18.8 / 23.4 | 43 | V35L (GTG→TTG) | gspC | Type II secretion system protein GspC |
| * | NC_000913 | 1,636,442 | 0 | C | G | 48.3% | 21.4 / 11.0 | 29 | intergenic (‑75/‑314) | nohA/ynfO | Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO |
| * | NC_000913 | 2,177,234 | 0 | C | A | 47.2% | 23.3 / 13.7 | 53 | intergenic (‑30/+278) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 707,984 | 0 | C | G | 47.1% | 7.9 / 18.3 | 34 | intergenic (+227/‑350) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 729,372 | 0 | A | C | 46.9% | 5.9 / 11.9 | 33 | intergenic (+32/‑211) | ybfA/rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| * | NC_000913 | 1,879,846 | 0 | T | G | 46.8% | 31.9 / 26.9 | 47 | T35P (ACG→CCG) | yeaR | DUF1971 domain‑containing protein YeaR |
| * | NC_000913 | 4,378,973 | 0 | G | C | 46.2% | ‑0.2 / 21.3 | 39 | intergenic (‑29/+34) | ampC/frdD | beta‑lactamase/fumarate reductase membrane protein FrdD |
| * | NC_000913 | 707,981 | 0 | C | T | 45.5% | 6.0 / 20.9 | 34 | intergenic (+224/‑353) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 2,470,436 | 0 | C | A | 45.5% | 38.1 / 10.1 | 44 | Q436K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 3,004,946 | 0 | G | T | 45.1% | 38.9 / 36.2 | 71 | Q281K (CAA→AAA) | ygeV | putative sigma(54)‑dependent transcriptional regulator YgeV |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 29 (0.380) | 12/256 | 3.9 | 30.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4118284 = | 67 (0.870) | intergenic (‑194/‑231) | glpF/zapB | glycerol facilitator/cell division factor ZapB | |||||
| * | ? | NC_000913 | = 1207805 | 63 (0.820) | 13 (0.190) | 10/224 | 3.9 | 18.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 62 (0.920) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 29 (0.380) | 8/256 | 5.1 | 28.7% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4118287 | 72 (0.940) | intergenic (‑197/‑228) | glpF/zapB | glycerol facilitator/cell division factor ZapB | |||||
| * | ? | NC_000913 | = 2067353 | NA (NA) | 11 (0.140) | 8/256 | 5.1 | 14.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4118284 = | 67 (0.870) | intergenic (‑194/‑231) | glpF/zapB | glycerol facilitator/cell division factor ZapB | |||||
| * | ? | NC_000913 | = 4542690 | 57 (0.740) | 4 (0.060) | 4/238 | 6.5 | 5.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 85 (1.190) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1467910 = | NA (NA) | 6 (0.080) | 4/256 | 6.8 | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1469241 | NA (NA) | intergenic (‑92/‑5) | insC‑2/ydbA | IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 3297415 | 35 (0.460) | 3 (0.040) | 3/250 | 7.3 | 6.2% | coding (724/1041 nt) | yraQ | permease family protein YraQ |
| ? | NC_000913 | 3987717 = | 56 (0.750) | coding (166/1197 nt) | hemY | protein HemY | |||||
| * | ? | NC_000913 | 2068944 = | NA (NA) | 5 (0.070) | 3/250 | 7.3 | NA | noncoding (1328/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2070275 | NA (NA) | intergenic (‑95/‑2) | insC‑3/yoeA | CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA | |||||
| * | ? | NC_000913 | 1467910 = | NA (NA) | 3 (0.040) | 3/256 | 7.4 | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1469242 | NA (NA) | intergenic (‑93/‑4) | insC‑2/ydbA | IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment | |||||