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 153 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 | 71.7% | 23.4 / 11.0 | 49 | 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 | 63.0% | ‑4.0 / 35.9 | 50 | Q433K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 2,177,255 | 0 | G | T | 58.9% | 3.0 / 41.4 | 56 | intergenic (‑51/+257) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 1,097,109 | 0 | A | T | 56.7% | ‑4.9 / 18.7 | 31 | intergenic (+280/+456) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 707,976 | 0 | T | G | 55.6% | 5.7 / 43.5 | 54 | intergenic (+219/‑358) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 3,491,693 | 0 | A | C | 55.0% | 6.4 / 18.5 | 20 | intergenic (‑73/+32) | yhfG/ppiA | DUF2559 domain‑containing protein YhfG/peptidyl‑prolyl cis‑trans isomerase A |
| * | NC_000913 | 2,177,221 | 0 | T | G | 54.9% | 7.9 / 42.9 | 51 | intergenic (‑17/+291) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 454,926 | 0 | G | T | 52.9% | 10.0 / 31.4 | 49 | intergenic (+137/‑207) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 454,919 | 0 | G | T | 52.2% | 33.2 / 55.7 | 51 | intergenic (+130/‑214) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 2,449,194 | 0 | A | C | 52.2% | ‑0.2 / 13.8 | 28 | intergenic (+37/+34) | smrB/yfcO | putative endonuclease SmrB/DUF2544 domain‑containing protein YfcO |
| * | NC_000913 | 454,906 | 0 | G | T | 51.2% | 4.5 / 31.9 | 50 | intergenic (+117/‑227) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 1,097,092 | 0 | T | C | 50.0% | ‑1.3 / 18.4 | 30 | intergenic (+263/+473) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,177,228 | 0 | C | T | 50.0% | ‑5.9 / 40.6 | 52 | intergenic (‑24/+284) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 2,470,436 | 0 | C | A | 48.9% | 28.5 / 15.3 | 48 | Q436K (CAA→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 2,470,411 | 0 | A | T | 47.1% | 27.7 / 31.9 | 51 | L427F (TTA→TTT) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 2,177,234 | 0 | C | T | 44.8% | 2.8 / 28.5 | 51 | intergenic (‑30/+278) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 454,873 | 0 | C | G | 42.9% | 27.2 / 28.5 | 57 | intergenic (+84/‑260) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 708,004 | 0 | C | A | 42.9% | 60.1 / 12.5 | 57 | intergenic (+247/‑330) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 707,981 | 0 | C | G | 42.4% | 29.4 / 21.7 | 56 | intergenic (+224/‑353) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 2,470,431 | 0 | G | T | 42.4% | 20.3 / 12.8 | 49 | R434I (AGA→ATA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| 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 | 4498181 = | NA (NA) | 11 (0.120) | 6/256 | 6.3 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+12/+81) | insD‑6/yjgX | KpLE2 phage‑like element; IS2 insertion element protein InsB/KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment | |||||
| * | ? | NC_000913 | 2996360 = | NA (NA) | 8 (0.090) +C |
6/254 | 6.3 | NA | pseudogene (1/399 nt) | ygeO | putative uncharacterized protein YgeO |
| ? | NC_000913 | = 2997691 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 13 (0.140) | 6/256 | 6.3 | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2070273 | NA (NA) | intergenic (‑93/‑4) | insC‑3/yoeA | CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA | |||||
| * | ? | NC_000913 | 381258 = | NA (NA) | 14 (0.150) | 6/254 | 6.3 | NA | pseudogene (3/417 nt) | yaiX | putative acyltransferase, N‑terminal fragment |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 731157 = | 102 (1.110) | 3 (0.030) | 3/248 | 7.8 | 2.7% | coding (1575/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | = 855588 | 117 (1.320) | coding (157/921 nt) | ldtB | L,D‑transpeptidase YbiS | |||||
| * | ? | NC_000913 | 628293 = | 101 (1.100) | 3 (0.030) | 3/250 | 7.8 | 3.4% | coding (600/858 nt) | entB | enterobactin synthase component B |
| ? | NC_000913 | 663005 = | 74 (0.830) | coding (959/1212 nt) | dacA | D‑alanyl‑D‑alanine carboxypeptidase DacA | |||||
| * | ? | NC_000913 | = 3593955 | 66 (0.720) | 3 (0.030) | 3/254 | 7.9 | 4.6% | coding (252/768 nt) | livG | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivG |
| ? | NC_000913 | = 3595143 | 59 (0.650) | coding (338/1278 nt) | livM | branched chain amino acid/phenylalanine ABC transporter membrane subunit LivM | |||||
| * | ? | NC_000913 | = 3152767 | 85 (0.930) | 3 (0.030) | 3/256 | 7.9 | 3.2% | coding (532/1188 nt) | metC | cystathionine beta‑lyase/L‑cysteine desulfhydrase |
| ? | NC_000913 | 3152773 = | 94 (1.030) | coding (538/1188 nt) | metC | cystathionine beta‑lyase/L‑cysteine desulfhydrase | |||||