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 168 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 | 68.5% | 23.3 / 15.7 | 59 | intergenic (‑41/+267) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 454,919 | 0 | G | T | 58.7% | 27.2 / 57.0 | 51 | intergenic (+130/‑214) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 1,097,109 | 0 | A | T | 58.3% | ‑3.9 / 16.0 | 26 | intergenic (+280/+456) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 4,378,973 | 0 | G | C | 57.1% | 0.2 / 20.9 | 35 | intergenic (‑29/+34) | ampC/frdD | beta‑lactamase/fumarate reductase membrane protein FrdD |
| * | NC_000913 | 4,082,697 | 0 | A | C | 55.6% | ‑3.8 / 17.1 | 41 | P21P (CCT→CCG) | fdoH | formate dehydrogenase O subunit beta |
| * | NC_000913 | 2,177,228 | 0 | C | G | 55.0% | ‑0.1 / 46.9 | 65 | intergenic (‑24/+284) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 2,177,255 | 0 | G | T | 54.2% | 3.9 / 40.8 | 59 | intergenic (‑51/+257) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 2,177,234 | 0 | C | A | 52.6% | 1.0 / 25.2 | 64 | intergenic (‑30/+278) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 454,906 | 0 | G | T | 52.5% | 22.8 / 42.8 | 46 | intergenic (+117/‑227) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 454,926 | 0 | G | T | 50.0% | 10.5 / 17.7 | 50 | intergenic (+137/‑207) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 2,177,221 | 0 | T | G | 50.0% | 9.7 / 38.9 | 62 | intergenic (‑17/+291) | 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% | 32.9 / 16.7 | 44 | Q433K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 4,283,228 | 0 | T | G | 48.5% | ‑4.1 / 13.9 | 40 | intergenic (‑153/+25) | yjcF/actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| * | NC_000913 | 1,097,092 | 0 | T | C | 47.8% | ‑1.0 / 14.4 | 24 | intergenic (+263/+473) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,139,598 | 0 | T | G | 41.9% | 36.5 / 22.0 | 75 | intergenic (+113/+161) | yegH/asmA | inner membrane protein YegH/putative assembly protein AsmA |
| * | NC_000913 | 1,331,189 | 0 | G | C | 40.8% | 93.7 / 40.1 | 76 | A48P (GCC→CCC) | topA | DNA topoisomerase 1 |
| * | NC_000913 | 2,470,431 | 0 | G | T | 40.6% | 32.1 / 10.2 | 41 | R434I (AGA→ATA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 2,519,212 | 0 | A | C | 40.5% | 69.3 / 37.1 | 79 | intergenic (+7/+45) | yfeD/gltX | putative DNA‑binding transcriptional regulator YfeD/glutamate‑‑tRNA ligase |
| * | NC_000913 | 2,031,625 | 0 | A | G | 40.5% | 49.5 / 22.9 | 45 | S231S (AGT→AGC) | dcm | DNA‑cytosine methyltransferase |
| * | NC_000913 | 1,829,568 | 0 | A | C | 40.0% | 66.8 / 17.7 | 66 | L56R (CTT→CGT) | astD | aldehyde dehydrogenase |
| 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 | = 1207805 | 95 (0.980) | 19 (0.220) | 16/224 | 3.1 | 21.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 52 (0.610) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207790 = | 106 (1.090) | 18 (0.210) | 16/224 | 3.1 | 19.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 55 (0.650) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 78 (0.800) | 12 (0.130) | 10/238 | 5.0 | 12.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 91 (1.010) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 78 (0.800) | 10 (0.110) | 8/238 | 5.7 | 11.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 89 (0.980) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1209618 | 82 (0.840) | 5 (0.060) | 4/226 | 7.3 | 5.6% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 95 (1.110) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | 1467910 = | NA (NA) | 4 (0.040) | 4/256 | 8.0 | 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 | |||||
| * | ? | NC_000913 | 555341 = | 83 (0.850) | 3 (0.030) | 3/256 | 8.7 | 4.2% | coding (731/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 2837552 | 53 (0.550) | intergenic (‑127/+26) | hypF/hydN | carbamoyltransferase HypF/putative electron transport protein HydN | |||||