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 65 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 | 67.6% | 5.2 / 14.3 | 40 | intergenic (‑41/+267) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 707,984 | 0 | C | G | 51.7% | 15.6 / 35.3 | 29 | intergenic (+227/‑350) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 2,177,255 | 0 | G | T | 51.2% | ‑2.7 / 34.2 | 41 | intergenic (‑51/+257) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 454,873 | 0 | C | G | 50.0% | ‑4.3 / 18.4 | 31 | intergenic (+84/‑260) | bolA/tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| * | NC_000913 | 707,981 | 0 | C | G | 47.8% | 12.4 / 12.3 | 29 | intergenic (+224/‑353) | glnS/chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| * | NC_000913 | 4,378,973 | 0 | G | C | 47.6% | ‑1.5 / 19.5 | 23 | intergenic (‑29/+34) | ampC/frdD | beta‑lactamase/fumarate reductase membrane protein FrdD |
| * | NC_000913 | 931,029 | 0 | G | C | 47.2% | 26.6 / 20.5 | 36 | intergenic (‑67/+56) | cydD/trxB | glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase |
| * | NC_000913 | 3,454,069 | 0 | G | T | 46.3% | 15.0 / 17.0 | 42 | Q444K (CAA→AAA) | gspA | Type II secretion system protein GspA |
| * | NC_000913 | 1,816,133 | 0 | A | C | 46.2% | 22.8 / 11.7 | 41 | intergenic (+5/+253) | katE/chbG | catalase II/chitin disaccharide deacetylase |
| * | NC_000913 | 931,028 | 0 | A | C | 44.7% | 24.4 / 15.7 | 39 | intergenic (‑66/+57) | cydD/trxB | glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase |
| * | NC_000913 | 2,519,212 | 0 | A | C | 44.7% | 19.7 / 21.9 | 38 | intergenic (+7/+45) | yfeD/gltX | putative DNA‑binding transcriptional regulator YfeD/glutamate‑‑tRNA ligase |
| * | NC_000913 | 361,307 | 0 | A | T | 43.9% | 25.3 / 20.4 | 42 | I185K (ATA→AAA) | lacA | galactoside O‑acetyltransferase |
| * | NC_000913 | 2,177,221 | 0 | T | G | 42.9% | 35.6 / 14.9 | 42 | intergenic (‑17/+291) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 2,470,444 | 0 | T | A | 41.7% | 10.1 / 12.9 | 24 | N438K (AAT→AAA) | yfdI | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| * | NC_000913 | 3,815,809 | 0 | G | C | 41.2% | 50.0 / 21.4 | 34 | intergenic (‑41/+54) | pyrE/rph | orotate phosphoribosyltransferase/truncated RNase PH |
| * | NC_000913 | 2,177,228 | 0 | C | G | 40.6% | 35.8 / 12.3 | 42 | intergenic (‑24/+284) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| * | NC_000913 | 3,407,971 | 0 | T | G | 39.5% | 39.3 / 15.8 | 39 | L122R (CTT→CGT) ‡ | panF | pantothenate:Na(+) symporter |
| * | NC_000913 | 3,407,970 | 0 | C | G | 36.8% | 49.7 / 13.3 | 38 | L122V (CTT→GTT) ‡ | panF | pantothenate:Na(+) symporter |
| * | NC_000913 | 2,725,829 | 0 | G | T | 36.6% | 54.9 / 28.8 | 41 | intergenic (‑83/+240) | kgtP/rrfG | alpha‑ketoglutarate:H(+) symporter/5S ribosomal RNA |
| * | NC_000913 | 3,455,671 | 0 | A | T | 36.2% | 38.7 / 19.7 | 47 | I32F (ATT→TTT) | gspC | Type II secretion system protein GspC |
| 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 | 4542682 = | 47 (0.740) | 5 (0.080) | 4/240 | 5.7 | 8.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 59 (0.990) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2070275 | NA (NA) | 4 (0.060) | 3/252 | 6.5 | 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 | 2996364 = | NA (NA) | noncoding (1328/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3186094 = | NA (NA) | 8 (0.130) | 3/258 | 6.6 | NA | pseudogene (70/71 nt) | yqiG | putative outer membrane usher protein YqiG |
| ? | NC_000913 | = 3187426 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 3 (0.050) | 3/258 | 6.6 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2996359 = | NA (NA) | pseudogene (2/399 nt) | ygeO | putative uncharacterized protein YgeO | |||||