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 239 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,177,245 | 0 | G | T | 60.8% | 5.9 / 19.8 | 57 | intergenic (‑41/+267) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 454,926 | 0 | G | T | 56.2% | 6.7 / 19.7 | 55 | intergenic (+137/‑207) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 2,177,234 | 0 | C | A | 55.6% | 2.2 / 42.5 | 65 | intergenic (‑30/+278) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 707,981 | 0 | C | G | 55.3% | 21.2 / 53.9 | 52 | intergenic (+224/‑353) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 454,906 | 0 | G | T | 53.7% | 15.4 / 39.0 | 51 | intergenic (+117/‑227) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 1,097,092 | 0 | T | C | 53.6% | ‑4.1 / 23.5 | 32 | intergenic (+263/+473) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,097,109 | 0 | A | T | 51.4% | 0.7 / 24.7 | 38 | intergenic (+280/+456) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,470,436 | 0 | C | A | 51.3% | 32.4 / 49.5 | 41 | Q436K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 4,283,228 | 0 | T | G | 51.2% | ‑4.0 / 14.4 | 51 | intergenic (‑153/+25) | yjcF/actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| * | NC_000913 | 454,919 | 0 | G | T | 51.0% | 31.7 / 54.1 | 57 | intergenic (+130/‑214) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 4,082,697 | 0 | A | C | 50.0% | 0.0 / 13.3 | 39 | P21P (CCT→CCG) | fdoH | formate dehydrogenase O subunit beta |
| * | NC_000913 | 454,933 | 0 | T | A | 47.3% | 11.7 / 29.8 | 56 | intergenic (+144/‑200) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 2,177,255 | 0 | G | T | 46.0% | 10.8 / 44.7 | 63 | intergenic (‑51/+257) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 4,283,226 | 0 | G | C | 46.0% | 47.3 / 20.8 | 50 | intergenic (‑151/+27) | yjcF/actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| * | NC_000913 | 2,470,427 | 0 | C | A | 45.2% | 48.2 / 15.0 | 44 | Q433K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 298,557 | 0 | A | C | 44.1% | 27.1 / 23.3 | 69 | L57R (CTC→CGC) | paoD | molybdenum cofactor insertion chaperone for PaoABC |
| * | NC_000913 | 1,816,133 | 0 | A | C | 43.5% | 35.3 / 12.8 | 52 | intergenic (+5/+253) | katE/chbG | catalase II/chitin disaccharide deacetylase |
| * | NC_000913 | 707,976 | 0 | T | G | 42.3% | 24.5 / 20.6 | 52 | intergenic (+219/‑358) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 1,636,442 | 0 | C | G | 41.4% | 62.4 / 26.2 | 61 | intergenic (‑75/‑314) | nohA/ynfO | Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO |
| * | NC_000913 | 1,636,447 | 0 | C | G | 41.1% | 68.0 / 21.2 | 60 | intergenic (‑80/‑309) | nohA/ynfO | Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO |
| 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 | 2288919 = | NA (NA) | 51 (0.460) | 22/256 | 3.2 | 34.7% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4118287 | 96 (0.870) | intergenic (‑197/‑228) | glpF/zapB | glycerol facilitator/cell division factor ZapB | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 12 (0.110) | 10/256 | 6.0 | 11.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4118287 | 96 (0.870) | intergenic (‑197/‑228) | glpF/zapB | glycerol facilitator/cell division factor ZapB | |||||
| * | ? | NC_000913 | = 2067353 | NA (NA) | 9 (0.080) | 7/250 | 7.0 | 8.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4118287 | 96 (0.870) | intergenic (‑197/‑228) | glpF/zapB | glycerol facilitator/cell division factor ZapB | |||||
| * | ? | NC_000913 | 4542682 = | 94 (0.850) | 5 (0.050) | 5/238 | 7.7 | 5.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 100 (0.970) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2066159 = | NA (NA) | 7 (0.060) | 5/250 | 8.0 | 6.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4118287 | 96 (0.870) | intergenic (‑197/‑228) | glpF/zapB | glycerol facilitator/cell division factor ZapB | |||||
| * | ? | NC_000913 | 781369 = | 123 (1.110) | 27 (0.250) +GAG |
4/250 | 8.5 | 24.0% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 52 (0.470) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | 781369 = | 123 (1.110) | 27 (0.250) +G |
4/254 | 8.6 | 22.0% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521128 | 70 (0.630) | intergenic (+2/‑45) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | = 1419335 | 148 (1.330) | 3 (0.030) | 3/238 | 8.8 | 2.2% | coding (122/135 nt) | ydaG | Rac prophage; uncharacterized protein YdaG |
| ? | NC_000913 | = 4257134 | 125 (1.210) | coding (20/609 nt) | lexA | DNA‑binding transcriptional repressor LexA | |||||
| * | ? | NC_000913 | = 1266789 | 98 (0.880) | 5 (0.050) | 3/234 | 8.8 | 4.7% | coding (696/834 nt) | prmC | protein‑(glutamine‑N(5)) methyltransferase |
| ? | NC_000913 | 3548869 = | 115 (1.130) | coding (1202/2085 nt) | malQ | 4‑alpha‑glucanotransferase | |||||
| * | ? | NC_000913 | = 762582 | 95 (0.860) | 3 (0.030) | 3/254 | 9.2 | 3.1% | coding (1061/1218 nt) | sucB | dihydrolipoyltranssuccinylase |
| ? | NC_000913 | 2730131 = | NA (NA) | noncoding (1027/1542 nt) | rrsG | 16S ribosomal RNA | |||||